Variants calling: CNV, PAV, and SV
#Packages
library(tidyverse)## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──## ✓ ggplot2 3.3.3 ✓ purrr 0.3.4
## ✓ tibble 3.1.0 ✓ dplyr 1.0.5
## ✓ tidyr 1.1.3 ✓ stringr 1.4.0
## ✓ readr 1.4.0 ✓ forcats 0.5.1## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()library(cowplot)
#Files and directories
dir_name = "/data2/alice/WW_project/"
metadata_dir=paste0(dir_name, "Metadata/")
list_dir="/home/alice/WW_PopGen/Keep_lists_samples/"
#Analysis directories
#____________________
data_dir=paste0(dir_name, "0_Data/")
assemb_dir = paste0(data_dir, "2_Denovo_assemblies/")
mito_gen_dir=paste0(data_dir, "4_Mitochondrial_genome/")
mito_blast=paste0(mito_gen_dir, "0_Mito_blast/")
mito_fasta=paste0(mito_gen_dir, "1_Mitochondrial_fastas/")
VAR_dir = paste0(dir_name, "1_Variant_calling/")
depth_per_window_dir = paste0(VAR_dir, "1_Depth_per_window/")
depth_per_gene_dir = paste0(VAR_dir, "2_Depth_per_gene/")
vcf_dir = paste0(VAR_dir, "4_Joint_calling/")
mito_SV = paste0(VAR_dir, "6_Mito_SV/")
PopStr_dir = paste0(dir_name, "2_Population_structure/")
mito_PS_dir = paste0(PopStr_dir, "1_Mitochondrial_genome/")
# Important files
#________________
Zt_list = read_tsv("/home/alice/WW_PopGen/Keep_lists_samples/Ztritici_global_March2021.genotyped.good_samples.args",
col_names = "ID_file")##
## ── Column specification ────────────────────────────────────────────────────────
## cols(
## ID_file = col_character()
## )metadata_cols = read_tsv("/home/alice/WW_PopGen/Keep_lists_samples/Main_table_from_SQL_Feb_2020_Description.tab",
col_names = F) %>% pull()##
## ── Column specification ────────────────────────────────────────────────────────
## cols(
## X1 = col_character()
## )metadata_file= read_tsv("/home/alice/WW_PopGen/Keep_lists_samples/Main_table_from_SQL_Feb_2020_with_collection.tab",
col_names = metadata_cols) ##
## ── Column specification ────────────────────────────────────────────────────────
## cols(
## .default = col_character(),
## X = col_double()
## )
## ℹ Use `spec()` for the full column specifications.mito_PS_dir = "/data2/alice/WW_project/0_Data/"
Sys.setenv(DATADIR=data_dir)
Sys.setenv(DEPTHGENEDIR=depth_per_gene_dir)
knitr::opts_chunk$set(message = F)
knitr::opts_chunk$set(warning = F)
knitr::opts_chunk$set(results = T)#Depth per chromosome I have run the depth per window for all chromosomes. From this data, I can extract summaries per chromosome per sample, per sample over the whole genome or per sample for the core chromosomes only.
list_file=$(ls -1 ${WINDEPTH}*.depth_per_window.q30.txt )
#Per sample per chromosome
echo -e "Sample\tCHROM\tMedian\tMean" > ${WINDEPTH}Depth_per_chromosome_summary.q30.txt
for p in $list_file ;
do
sed "s/:/\t/g" $p | ~/Software/bedtools groupby -g 1,2 -o median,mean -c 5;
done >> ${WINDEPTH}Depth_per_chromosome_summary.q30.txt
#Per sample
echo -e "Sample\tMedian\tMean" > ${WINDEPTH}Depth_per_sample_summary.q30.txt
for p in $list_file ;
do
sed "s/:/\t/g" $p | ~/Software/bedtools groupby -g 1 -o median,mean -c 5;
done >> ${WINDEPTH}Depth_per_sample_summary.q30.txt
#Per sample on core chromosomes
echo -e "Sample\tMedian\tMean" > ${WINDEPTH}Depth_per_sample_core_chr_summary.q30.txt
for p in $list_file ;
do
sed "s/:/\t/g" $p | \
awk 'BEGIN {FS = "\t"; OFS = "\t"} $2 < 14 {print}' | \
~/Software/bedtools groupby -g 1 -o median,mean -c 5
done >> ${WINDEPTH}Depth_per_sample_core_chr_summary.q30.txt
Such summaries per chromosomes are very useful to visualize if some samples have multiple copies of a chromosomes or the presence/absence of chromosomes in particular for the accessory chromosomes.
# Reading in the summarized data
core_depth = read_tsv(paste0(depth_per_window_dir, "Depth_per_sample_core_chr_summary.q30.txt")) %>%
mutate(Median_core = Median) %>%
inner_join(., Zt_list, by = c("Sample" = "ID_file"))
chrom_depth = read_tsv(paste0(depth_per_window_dir, "Depth_per_chromosome_summary.q30.txt")) %>%
left_join(., core_depth %>% select(Sample, Median_core)) %>%
mutate(Relative_depth = as.numeric(Median)/as.numeric(Median_core)) %>%
inner_join(., Zt_list, by = c("Sample" = "ID_file"))
# Heatmap of the depth per chromosome
heatmap_depth = chrom_depth %>%
filter(CHROM != "mt") %>%
ggplot(aes(x = as.numeric(CHROM), y=Sample, fill=Relative_depth)) +
geom_tile() + scale_fill_gradient2(low="white", high = "#479DAE") +
geom_vline(xintercept = 13.5, linetype = "longdash", colour = "gray20") +
theme(axis.text.y = element_blank(),
axis.title.y = element_blank(), axis.ticks.y=element_blank()) +
labs(fill = "Depth", x= "Chromosome") + xlim(c(0.5, 21.5))
ggplot(data = chrom_depth, aes(Relative_depth)) +
geom_density(col = "#16697a", fill = "#16697a", alpha =0.4) +
facet_wrap(vars(as.numeric(CHROM)), scales = "free") +
theme_classic() +
geom_vline(xintercept = 0.2, col = "#ffa62b")
# Estimation of low and high depth chromosomes
# (as proxy for present in 0 or multiple copies)
Lthres = 0.20
Hthres = 1.50
depth = chrom_depth %>%
filter(CHROM != "mt") %>%
dplyr::mutate(Depth_is = ifelse(Relative_depth > Hthres, "High",ifelse(Relative_depth < Lthres, "Low", "Normal")))
# Barplot
bar_Ndepth_per_CHR =ggplot(depth, aes(x = as.numeric(CHROM), fill = Depth_is)) +
geom_bar(stat = "count") +
scale_fill_manual(values = c("#16697a", "#82c0cc", "#EDE7E3")) +
theme_light()+
labs(x= "Chromosome", y = "Number of isolates")
# Lollipop plots
##For low normalized depth values
temp = depth %>%
filter(Depth_is == "Low") %>%
dplyr::group_by(CHROM) %>%
dplyr::count()
lollow = ggplot(temp, aes(x = as.character(CHROM), y = n)) +
geom_segment( aes(x=as.character(CHROM), xend=as.character(CHROM), y=0, yend=max(temp$n)),
color="grey80", size = 1) +
geom_segment( aes(x=as.character(CHROM), xend=as.character(CHROM), y=0, yend=n),
color="grey20", size = 1) +
geom_point( color="#82c0cc", size=4) +
geom_text(aes( label = n,
y= n), stat= "identity",
hjust = -0.5, vjust = -0.2) +
theme_light() +
theme(
panel.grid.major.y = element_blank(),
panel.border = element_blank(),
axis.ticks.x = element_blank(),
axis.text.x = element_text(size = 10),
axis.text.y = element_text(size = 10)
) +
ylim(c(0,max(temp$n)+ max(temp$n)*0.1)) +
labs( x= "Chromosome", y = "Number of isolates without chromosome") +
coord_flip()
# Gathering all 3 plots into a single figure
bottom_row <- cowplot::plot_grid(bar_Ndepth_per_CHR + theme(legend.position = "bottom"), lollow,
labels = c('B', 'C'), label_size = 12, ncol = 2)
cowplot::plot_grid(heatmap_depth, bottom_row, labels = c('A', ''), label_size = 12, ncol = 1)
Depth per window and GC bias
I have used the bedtools nuc option to estimate the GC content per 1kb-window for the whole reference IPO323 genome
GC_per_window = read_tsv(paste0(data_dir, "Zymoseptoria_tritici.MG2.dna.toplevel.mt+.1kb_windows.nuc_GC.tab")) %>%
mutate(GC = round(`5_pct_gc`, 2)) %>%
filter( !is.na(`#1_usercol`))
temp = GC_per_window %>%
filter(`#1_usercol` < 14) %>%
dplyr::select(CHROM = `#1_usercol`, Win_start = `2_usercol`, Win_stop = `3_usercol`, GC) %>%
group_by(GC) %>%
count()
# Histogram of GC values
xint = median(GC_per_window$GC)
temp %>%
ggplot(aes(x = GC, y = n, fill = n > 40)) +
geom_bar(stat = "identity") +
theme_light() +
scale_fill_manual(values =c( "#82c0cc", "#EDE7E3"))+
geom_vline(xintercept = xint, col = "#82c0cc") +
annotate("text", label = paste0("Median GC is ", xint),
x = xint - xint*0.2, y = 5200,
size = 4, colour = "#82c0cc", fontface = "bold")
GC_avail = temp %>% filter(n > 40) %>% dplyr::select(GC) %>% pull()
random_GC_windows = GC_per_window %>%
dplyr::select(CHROM = `#1_usercol`, Win_start = `2_usercol`, Win_stop = `3_usercol`, GC) %>%
filter(GC %in% GC_avail)%>%
group_by(GC) %>%
sample_n(40) %>%
mutate(CHROM = as.character(CHROM),
Win_start = as.character(Win_start),
Win_stop = as.character(Win_stop))The distribution of GC is slightly skewed in the GC-rich side, with a median above 0.5. However, there is an AT-rich fat tail, or even a bimodal distribution. These windows are most probably containing RIP-affected repeated regions.
From there, we need to know if the different collections present GC bias in their sequencing. We expect a batch effect in the sequencing here since we have data coming from a lot of different years and labs (and because batch effect happens in general).
files <- list.files(depth_per_window_dir, pattern = "depth_per_window.q30.txt$", full.names = T)
depth_per_win = files %>%
map_dfr(~read_tsv(., col_names = c("temp", "Depth")) %>%
separate(col = temp, into = c("ID_file", "CHROM", "Win_start", "Win_stop"),
sep = ":") %>%
inner_join(., random_GC_windows)) %>%
left_join(., Zt_list)
write_tsv(depth_per_win, paste0(depth_per_window_dir, "Depth_for_GC_bias.txt"))depth_per_win = read_tsv(paste0(depth_per_window_dir, "Depth_for_GC_bias.txt"))
scale_this <- function(x){
(x - mean(x, na.rm=TRUE)) / sd(x, na.rm=TRUE)
}
GC_coverage = depth_per_win %>%
filter(Depth > 0) %>%
group_by(ID_file) %>%
dplyr::mutate(scaled_depth = scale_this(Depth)) %>%
filter(!is.na(scaled_depth))
#GC bias estimation
getAlpha<-function(i){
#print(i)
temp = GC_coverage %>%
filter(ID_file == i) #%>%
#mutate(log_depth = log(Depth))
if (nrow(temp) < 10) {
return(NA)} else {
linearMod <- lm(scaled_depth ~ GC, data=temp) # build linear regression model on full data
alpha = linearMod$coefficients["GC"]
return (alpha)}}
v_getAlpha <- Vectorize(getAlpha)
GC_bias = GC_coverage %>%
dplyr::select(ID_file) %>%
distinct() %>%
dplyr::mutate(GC_bias_slope = v_getAlpha(ID_file)) %>%
left_join(., metadata_file %>% select(ID_file, Collection, Continent, Country, Region,
Sampling_Date, Latitude, Longitude))
write_tsv(GC_bias, paste0(depth_per_window_dir, "GC_bias_per_sample.txt"))
ggplot(GC_bias, aes(GC_bias_slope)) +
geom_density() +
theme_bw()
#GC bias illustration
GC_coverage %>%
filter(ID_file %in% sample(GC_coverage$ID_file, 15)) %>%
ggplot(aes(GC, Depth)) +
geom_point(col = "grey", alpha = 0.4) +
scale_fill_continuous(type = "viridis") +
theme_bw() + facet_wrap(~ID_file, scale = "free") +
geom_smooth(method = "lm", se = FALSE,
color = "goldenrod", size= 0.7) +
labs(x = "GC percent per window",
y = "Depth per window",
title = "Illustration of the GC bias",
subtitle = "I use the slope of a linear model to infer the GC bias.")
#GC bias per collection
temp = GC_bias %>%
filter(Collection != "\\N") %>%
group_by(Collection) %>%
count() %>%
filter(n >= 20)
GC_bias_violins = inner_join(temp, GC_bias) %>%
group_by(Collection) %>%
mutate(Median = median(GC_bias_slope)) %>%
ggplot(., aes(x = reorder(Collection, Median), y = GC_bias_slope, fill = reorder(Collection, Median))) +
geom_violin(alpha = .7) +
theme_bw() +
theme(axis.text.x = element_text(angle = 30, vjust = 1, hjust = 1),
plot.margin = unit(c(0.5, 0.5, 0.5, 1), "cm")) +
labs(x = "Collection", y = "GC bias estimate")
GC_bias_violins
It is very clear that we do have a batch effect but also that some datasets are very, very biased. The older Hartmann data (also called Qst population) in particular is strongly biased.
Depth per gene
Aside from the depth per window, I have also estimated the depth of coverage per gene. I want to infer some gene presence/absence based on the depth so I need to normalize the depth. I have tried to normalize simply based on the depth over the core chromosomes in general, but this resulted in a median normalized depth per gene at 1.1 instead of 1 as expected. This is probably due to lower coverage in intergenic regions (in particular repeated regions that might be more suspectible to being deleted in some strains). The overall coverage for the chromosome would thus be lower than the coverage for the genes of the same chromosome.
I have chosen to normalize using the median depth of genes for the core chromosomes. This resulted in a normalized depth with a median around one as shown with a sample of 4 isolates.
files <- list.files(depth_per_gene_dir, pattern = "depth_per_gene.q30.txt$", full.names = T)
depth_per_gene = sample(files, size = 4) %>%
map_dfr(~read_tsv(., col_names = c("temp", "Depth")) %>%
separate(col = temp, into = c("Sample", "CHROM", "Gene"), sep = ":")) %>%
left_join(., metadata_file, c("Sample" = "ID_file"))
temp = depth_per_gene %>%
filter(str_detect(Gene, "_TU_")) %>%
filter( !str_detect(Gene, "Parent")) %>%
filter(as.numeric(CHROM) < 14) %>%
group_by(Sample) %>%
summarize(Median_core = median(Depth))
depth_per_gene %>%
inner_join(., temp) %>%
mutate(Norm_median_depth = Depth / Median_core) %>%
filter(str_detect(Gene, "_TU_")) %>%
filter( !str_detect(Gene, "Parent")) %>%
ggplot(aes(x = Norm_median_depth, fill = Sample, col = Sample)) +
geom_density(alpha = 0.4) +
geom_vline(xintercept = 1, col = "black", linetype = "dashed") +
facet_wrap(vars(as.numeric(CHROM)), scales ="free") +
theme_bw()+
labs(title = "Normalized with the depth of the core chromosomes genes",
x = "Normalized depth of coverage per gene")
Once I am confident that the normalization I am using is appropriate, I do this for all genes.
files <- list.files(depth_per_gene_dir, pattern = "depth_per_gene.q30.txt$", full.names = T)
depth_per_gene = files %>%
map_dfr(~read_tsv(., col_names = c("temp", "Depth")) %>%
separate(col = temp, into = c("Sample", "CHROM", "Gene"), sep = ":"))
temp = depth_per_gene %>%
filter(str_detect(Gene, "_TU_")) %>%
filter( !str_detect(Gene, "Parent")) %>%
filter(as.numeric(CHROM) < 14) %>%
group_by(Sample) %>%
summarize(Median_core = median(Depth))
depth_per_gene = depth_per_gene %>%
inner_join(., temp) %>%
mutate(Norm_median_depth = round(Depth / Median_core, 2)) %>%
filter(str_detect(Gene, "_TU_")) %>%
filter( !str_detect(Gene, "Parent")) %>%
separate(col = Gene, into = c("ID", "Name"), sep = ";") %>%
select(-ID) %>%
mutate(Name = str_replace(Name, "Name=", ""))
write_tsv(depth_per_gene, paste0(depth_per_gene_dir, "Depth_per_genes_normalized.txt"))Depth for resequencing pairs
depth_per_gene = read_tsv(paste0(depth_per_gene_dir, "Depth_per_genes_normalized.txt"))
repeat_seq = read_delim(paste0(list_dir, "Repeat_sequencing.txt"), col_names = c("Seq1", "Seq2"), delim = " ") %>%
mutate(Pair = paste0("Pair_", c(1:length(Seq1)))) %>%
pivot_longer(-Pair, names_to = "temp", values_to = "ID_file") %>%
#dplyr::select(-temp) %>%
left_join(., GC_bias) %>%
mutate(Collection = ifelse(is.na(Collection), "ETHZ_2020", Collection))
repeat_collec = unique(repeat_seq$Collection)
depth_per_gene %>%
select(Sample, Median_core) %>%
distinct() %>%
inner_join(., GC_bias, by = c("Sample" = "ID_file")) %>%
filter(Collection %in% repeat_collec) %>%
group_by(Collection) %>%
mutate(Median = median(GC_bias_slope)) %>%
ggplot(.) +
geom_violin(aes(x = reorder(Collection, Median), y = GC_bias_slope), alpha = .7) +
theme_bw() +
theme(axis.text.x = element_text(angle = 30, vjust = 1, hjust = 1),
plot.margin = unit(c(0.5, 0.5, 0.5, 1), "cm")) +
labs(x = "Collection", y = "GC bias estimate") +
geom_point(data = repeat_seq, aes(col = Pair, x = Collection, y = GC_bias_slope))
temp2 = repeat_seq %>%
dplyr::select(Pair, temp, GC_bias_slope) %>%
pivot_wider(names_from = temp, values_from = GC_bias_slope)
pair_GC_plot = ggplot(data = repeat_seq, aes(y = Pair, x = GC_bias_slope)) +
geom_point(aes(col = Collection)) +
geom_segment(data = temp2, aes(y = Pair, yend = Pair, x = Seq1, xend = Seq2)) +
theme_bw() +
labs(x = "GC bias estimation", y = element_blank())TE = read_delim("/data2/alice/WW_project/4_TE_RIP/0_RIP_estimation/Nb_reads_repeat_sequencing.txt", delim = " ") %>%
mutate(Percent_TE_reads = 100*Te_aligned_reads/Genome_aligned_reads) %>%
inner_join(repeat_seq)
#Plot TE content
seg_TE = TE %>% dplyr::select(Pair, temp, Percent_TE_reads) %>% pivot_wider(names_from = temp, values_from = Percent_TE_reads)
pair_TE_plot = ggplot(data = TE, aes(y = Pair, x = Percent_TE_reads)) +
geom_point(aes(col = Collection)) +
geom_segment(data = seg_TE, aes(y = Pair, yend = Pair, x = Seq1, xend = Seq2)) +
theme_bw() +
labs(x = "TE content estimation", y = element_blank())
#Get legend and put plots together
legend = get_legend(pair_GC_plot + theme(legend.position = "bottom"))
row_plot = cowplot::plot_grid(pair_GC_plot + theme(legend.position = "none"),
pair_TE_plot + theme(legend.position = "none"),
ncol = 2, labels = c("A", "B"))
cowplot::plot_grid(row_plot, legend, rel_heights = c(10, 1), ncol = 1)
genes_pairs = paste0(depth_per_gene_dir, unique(repeat_seq$ID_file), ".depth_per_gene.q30.txt") %>%
map_dfr(~read_tsv(., col_names = c("temp", "Depth")) %>%
separate(col = temp, into = c("ID_file", "CHROM", "Gene"), sep = ":"))
temp = genes_pairs %>%
filter(str_detect(Gene, "_TU_")) %>%
filter( !str_detect(Gene, "Parent")) %>%
filter(as.numeric(CHROM) < 14) %>%
group_by(ID_file) %>%
summarize(Median_core = median(Depth))
genes_pairs = genes_pairs %>%
inner_join(., temp) %>%
#mutate(Norm_median_depth = round(Depth / Median_core)) %>%
mutate(Norm_median_depth = ifelse(Depth / Median_core < 0.25, 0,
ifelse(Depth / Median_core > 1.75, 2, 1))) %>%
filter(str_detect(Gene, "_TU_")) %>%
filter( !str_detect(Gene, "Parent")) %>%
separate(col = Gene, into = c("ID", "Name"), sep = ";") %>%
select(-ID) %>%
mutate(Name = str_replace(Name, "Name=", "")) %>%
full_join(., repeat_seq)
temp = genes_pairs %>%
dplyr::select(Pair, temp, Name, Norm_median_depth) %>%
pivot_wider(names_from = temp, values_from = Norm_median_depth) %>%
mutate(diff = abs(Seq1 - Seq2))
p1 = temp %>%
group_by(Pair) %>%
count(diff) %>%
pivot_wider(names_from = diff, values_from = n) %>%
ggplot(aes(x = Pair, y = `1`, fill = Pair)) +
geom_bar(stat = "identity") +
theme_bw() +
labs(y = "Number of genes", x = "",
subtitle = "Genes with a different CNV value per pair")
p2 = temp %>%
filter(diff > 0) %>%
group_by(Name) %>%
count() %>%
ggplot(aes(n)) +
geom_histogram(bins = 6) +
theme_bw() +
labs(y = "Number of genes", x = "Number of pairs",
subtitle = "Genes with a difference CNV value shared between pairs")
row1 = cowplot::plot_grid(p1 + theme(legend.position = "none"), p2, ncol = 2, labels = c("A", "B"))
p3 = genes_pairs %>%
filter(Norm_median_depth != 1) %>%
group_by(ID_file, Norm_median_depth) %>%
count()%>%
ggplot(aes(x = ID_file, y = n, fill = as.character(Norm_median_depth))) +
geom_bar(stat = "identity") +
theme_bw() +
theme(axis.text.x = element_text(angle = 25, hjust = 1, vjust = 1),
plot.margin = unit(c(0.5, 0.5, 0.5, 1.5), "cm")) +
labs(y = "Number of genes", x = element_blank(),
fill = "CNV")
cowplot::plot_grid(row1, p3, ncol =1, labels = c("", "C"))
# head -n1 /data2/alice/WW_project/1_Variant_calling/2_Depth_per_gene/global_IPO-CNV.seg.gene.table \
# > /data2/alice/WW_project/1_Variant_calling/2_Depth_per_gene/global_IPO-CNV.seg.gene.reseq_only.tab
# grep -f WW_PopGen/Keep_lists_samples/Repeat_sequencing.args \
# /data2/alice/WW_project/1_Variant_calling/2_Depth_per_gene/global_IPO-CNV.seg.gene.table | cut -f 2- \
# >> /data2/alice/WW_project/1_Variant_calling/2_Depth_per_gene/global_IPO-CNV.seg.gene.reseq_only.tab
genes_pairs_Sabina = read_csv(paste0(depth_per_gene_dir, "Sabina_gcnv_event.reseq_only.csv")) %>%
full_join(., repeat_seq, by = c("sample" = "ID_file"))
temp = genes_pairs_Sabina %>%
dplyr::select(Pair, temp, ref_gene, event) %>%
filter(temp != "NA") %>%
distinct() %>%
pivot_wider(names_from = temp, values_from = event) %>%
mutate(Comparison = ifelse( Seq1 == Seq2, "OK", "Different"))
p1 = temp %>%
filter(Comparison == "Different") %>%
group_by(Pair) %>%
count() %>%
ggplot(aes(x = Pair, y = n, fill = Pair)) +
geom_bar(stat = "identity") +
theme_bw() +
labs(y = "Number of genes", x = "",
subtitle = "Genes with a different CNV value per pair")
p2 = left_join(genes_pairs_Sabina, temp) %>%
filter(!is.na(Comparison)) %>%
filter(Seq1 != "P" | Seq2 != "P") %>%
ggplot(aes(x = Pair, y = QS, fill = Comparison, color = Comparison)) +
geom_violin() +
scale_fill_manual(values =c( "#82c0cc", "#EDE7E3")) +
scale_color_manual(values =c( "#82c0cc", "#EDE7E3")) +
theme_cowplot() +
labs(x = element_blank(), y = "Variants quality") +
theme(axis.text = element_text(size = 10),
axis.title = element_text(size = 12))
p3 = left_join(genes_pairs_Sabina, temp) %>%
filter(!is.na(Comparison)) %>%
ggplot(aes(x = Pair, y = QS, fill = Comparison, color = Comparison)) +
geom_violin() +
scale_fill_manual(values =c( "#82c0cc", "#EDE7E3")) +
scale_color_manual(values =c( "#82c0cc", "#EDE7E3")) +
theme_cowplot() +
labs(x = element_blank(), y = "All genes quality") +
theme(axis.text = element_text(size = 10),
axis.title = element_text(size = 12))
legend_b = get_legend(p3 + theme(legend.position = "bottom"))
col2 = cowplot::plot_grid(p2 + theme(legend.position = "none"),
p3 + theme(legend.position = "none"),
legend_b,
ncol = 1, rel_heights = c(1, 1, 0.4))
cowplot::plot_grid(p1+ theme(legend.position = "none"), col2, ncol = 2)
threshold_QS = 1000
Sys.setenv(threshold_QS=threshold_QS)
filtered_comparison = left_join(genes_pairs_Sabina, temp) %>%
filter(!is.na(Comparison)) %>%
filter(Seq1 != "P" | Seq2 != "P")
filtered_comparison %>%
ggplot(aes(x = Comparison, y = QS, fill = Comparison)) +
geom_violin() +
geom_boxplot(width = 0.03, fill = "white") +
scale_fill_manual(values =c( "#82c0cc", "#EDE7E3")) +
theme_cowplot() +
labs(x = element_blank(), y = "Variants quality") +
theme(axis.text = element_text(size = 10),
axis.title = element_text(size = 12))
filtered_comparison %>%
ggplot(aes(x = QS, fill = Comparison)) +
geom_density(alpha = 0.6) +
scale_fill_manual(values =c( "#82c0cc", "#EDE7E3")) +
theme_cowplot() +
labs(x = element_blank(), y = "Variants quality") +
theme(axis.text = element_text(size = 10),
axis.title = element_text(size = 12)) +
geom_vline(xintercept = threshold_QS)
summary_filtered = filtered_comparison %>%
group_by(Comparison) %>%
count(QS > threshold_QS)
summary_filtered %>%
ggplot(aes(x = Comparison, y = n, fill = `QS > threshold_QS`)) +
geom_bar(stat = "identity") +
theme_cowplot() +
scale_fill_manual(values =c( "#EDE7E3", "#82c0cc" )) +
geom_label(data = summary_filtered %>% filter(`QS > threshold_QS`),
mapping = aes(x = Comparison, y = n + 1000 , label = n))
awk -v threshold=${threshold_QS} 'BEGIN {FS = ","; OFS = "\t"} $9 > threshold {print $1,($2 + $3)/2,$4,$5,$15 } ' \
${DEPTHGENEDIR}Sabina_gcnv_event.csv \
> ${DEPTHGENEDIR}Sabina_gcnv_event.filtered.tsv#temp = read_tsv(file = paste0(depth_per_gene_dir, "Sabina_gcnv_event.filtered.tsv"),
# col_names = c("CHROM", "POS", "Gene", "Sample", "Allele"), skip = 1) %>%
# pivot_wider(names_from = Sample, values_from = Allele, values_fill = ".")
variant_list = read_tsv(file = paste0(depth_per_gene_dir, "Sabina_gcnv_event.filtered.tsv"),
col_names = c("CHROM", "POS", "Gene", "Sample", "Allele"), skip = 1) %>%
filter(Sample %in% Zt_list$ID_file) %>%
mutate(POS = round(POS)) %>%
group_by(CHROM, POS, Gene) %>%
dplyr::count(Allele) %>%
mutate(Nb_allele = n()) %>%
pivot_wider(names_from = Allele, values_from = n, values_fill = 0) %>%
mutate(max = max(M, P, D, PD, PM), sum = sum(M, P, D, PD, PM))
temp = depth_per_gene %>% filter(Sample %in% Zt_list$ID_file) %>%
mutate(Norm_median_depth = as.numeric(Norm_median_depth)) %>%
mutate(Allele = ifelse(Norm_median_depth < 0.25, "D",
ifelse(Norm_median_depth > 1.75, "M", "P"))) %>%
group_by(CHROM, Name) %>% dplyr::count(Allele) %>% mutate(Nb_allele = n()) %>%
pivot_wider(names_from = Allele, values_from = n, values_fill = 0) %>%
mutate(max = max(M, P, D), sum = sum(M, P, D))
table(temp$Nb_allele)##
## 1 2 3
## 4937 5106 1796table(variant_list$Nb_allele)##
## 1 2 3 4 5
## 5994 4637 1036 161 3bind_rows(temp %>% mutate(Method = "Alice"), variant_list %>% mutate(Method = "Sabina")) %>%
filter(Nb_allele > 1) %>%
ggplot(aes(x = max, fill = Method, col = Method)) +
geom_density(alpha = 0.4) +
theme_bw()
Alice_CNV_per_sample = depth_per_gene %>% filter(Sample %in% Zt_list$ID_file) %>%
mutate(Norm_median_depth = as.numeric(Norm_median_depth)) %>%
mutate(Allele = ifelse(Norm_median_depth < 0.25, "D",
ifelse(Norm_median_depth > 1.25, "M", "P"))) %>%
filter(CHROM < 14) %>%
group_by(Sample) %>% dplyr::count(Allele) %>%
pivot_wider(names_from = Allele, values_from = n, values_fill = 0) %>%
mutate(max = max(M, D), sum = sum(M, D)) %>%
mutate(Method = "Alice")
Sabina_CNV_per_sample = read_tsv(file = paste0(depth_per_gene_dir, "Sabina_gcnv_event.filtered.tsv"),
col_names = c("CHROM", "POS", "Gene", "Sample", "Allele"), skip = 1) %>%
filter(Sample %in% Zt_list$ID_file) %>%
filter(CHROM < 14) %>%
mutate(POS = round(POS)) %>%
group_by(Sample) %>% dplyr::count(Allele) %>%
pivot_wider(names_from = Allele, values_from = n, values_fill = 0) %>%
mutate(max = max(M, D, PD, PM), sum = sum(M, D, PD, PM)) %>%
mutate(Method = "Sabina")
write_tsv(Sabina_CNV_per_sample,
file = paste0(depth_per_gene_dir, "Sabina_gcnv_event.filtered.core_chr.per_sample.tsv"))
bind_rows(Alice_CNV_per_sample, Sabina_CNV_per_sample) %>%
ggplot(aes(x = sum, col = Method, fill = Method)) +
geom_density(alpha =.4) +
theme_bw()
full_join(Alice_CNV_per_sample %>% dplyr::select(Sample, variant_Alice = sum),
Sabina_CNV_per_sample %>% dplyr::select(Sample, variant_Sabina = sum)) %>%
ggplot(aes(x = variant_Alice, y = variant_Sabina)) +
geom_point() +
theme_bw() +
geom_abline(intercept = 0, slope = 1)
bind_rows(Alice_CNV_per_sample, Sabina_CNV_per_sample) %>% dplyr::select(-sum, -max, -P) %>% pivot_longer(-c(Sample, Method), names_to = "Variant_type", values_to = "Count") %>% ggplot(aes(fill = Method, col = Method, x = Variant_type, y = log2(Count))) + geom_violin(alpha = .4) + theme_bw()
annot = read_tsv(paste0(data_dir, "Annotations_2018_genomes_for_publication.tab")) %>%
filter(Sample == "Zt09")
effectors = annot %>% filter(Effector == "Effector") %>% select(Protein_ID) %>% pull()
effector_CNV = read_tsv(file = paste0(depth_per_gene_dir, "Sabina_gcnv_event.filtered.tsv"),
col_names = c("CHROM", "POS", "Gene", "Sample", "Allele")) %>%
mutate(Gene = str_replace(Gene, "TU", "chr")) %>%
filter(Gene %in% effectors)
# inner_join(., effectors, by = c("ref_gene" = "Protein_ID"))
ggplot(effector_CNV, aes(x = Gene, y = Sample, fill = Allele)) +
geom_tile() +
theme_cowplot() +
theme()
temp = left_join(effector_CNV, metadata_file, by = c("Sample" = "ID_file")) %>%
mutate(Sample = fct_reorder(Sample, Sampling_Date)) %>%
mutate(Sample = fct_reorder(Sample, Country)) %>%
mutate(Sample = fct_reorder(Sample, Continent))
heatmap_CNV = temp %>%
ggplot(aes(x = Gene, y = Sample, fill = Allele)) +
geom_tile() +
theme(axis.text.y = element_blank(), axis.ticks.y=element_blank(), axis.title.y = element_blank(),
axis.text.x = element_blank(), axis.ticks.x=element_blank()) +
scale_fill_manual(values = c("gold", "darkred", "grey90", "yellow", "red"))
plot_continent = ggplot(data = temp, aes(x = 1, y=Sample, fill=Continent)) +
geom_tile(aes(width = 2)) +
theme_classic() +
theme(axis.text.y = element_blank(), axis.ticks.y=element_blank(),
legend.position="left",
axis.text.x=element_text(colour="white")) +
scale_fill_brewer(palette = "Dark2") +
labs(y= "Isolate")
plot_grid(plot_continent, heatmap_CNV, rel_widths = c(2, 5))
CAZymes = annot %>% filter(CAZyme_family != "-") %>% select(Protein_ID) %>% pull()
CAZymes_CNV = read_tsv(paste0(depth_per_gene_dir, "Sabina_gcnv_event.filtered.simplified.tsv")) %>%
filter(ref_gene %in% CAZymes)
# inner_join(., effectors, by = c("ref_gene" = "Protein_ID"))
temp = left_join(CAZymes_CNV, metadata_file, by = c("sample" = "ID_file")) %>%
ungroup() %>%
#mutate(sample = fct_reorder(sample, Sampling_Date)) %>%
#mutate(sample = fct_reorder(sample, Country)) %>%
mutate(sample = fct_reorder(sample, Continent))
heatmap_CNV2 = temp %>%
ggplot(aes(x = ref_gene, y = reorder(sample, Continent), fill = event)) +
geom_tile() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank(), axis.title.y = element_blank(),
axis.text.x = element_blank(), axis.ticks.x = element_blank())
plot_continent = ggplot(data = temp, aes(x = 1, y = reorder(sample, Continent), fill = reorder(sample, Continent))) +
geom_tile(aes(width = 2)) +
theme_classic() +
theme(axis.text.y = element_blank(), axis.ticks.y = element_blank(),
legend.position ="left",
axis.text.x = element_text(colour = "white")) +
scale_fill_brewer(palette = "Dark2") +
labs(y = "Isolate")
plot_continent
plot_grid(plot_continent, heatmap_CNV2, rel_widths = c(2, 5))
De novo assemblies
Whole genome assembly statistics and filtering
while read sample;
do
echo $sample;
python ~/Common_scripts/Rename_fragments_in_fasta.py \
--input /data2/alice/WW_project/0_Data/2_Denovo_assemblies/${sample}/scaffolds.fasta \
-o /data2/alice/WW_project/0_Data/2_Denovo_assemblies/${sample}.fasta \
--sample_name ${sample} --format spades --match_length_lines ;
done < Keep_lists_samples/Assembled.sample_list.argsecho -e "Sample\tAssembly_type\tEstimate\tValue" > /data2/alice/WW_project/0_Data/2_Denovo_assemblies/Stats_filtered_assemblies.tab ;
while read sample;
do
echo $sample;
python /home/alice/Common_scripts/Stats_from_fasta.py \
/data2/alice/WW_project/0_Data/2_Denovo_assemblies/${sample}.fasta;
cat /data2/alice/WW_project/0_Data/2_Denovo_assemblies/${sample}.fasta_stats.txt | \
awk -v sample=$sample 'BEGIN{FS = "\t"; OFS = "\t"} {print sample, "Filtered", $1, $2} ' >> \
/data2/alice/WW_project/0_Data/2_Denovo_assemblies/Stats_filtered_assemblies.tab ;
done < Keep_lists_samples/Assembled.sample_list.args
echo -e "Sample\tAssembly_type\tEstimate\tValue" > /data2/alice/WW_project/0_Data/2_Denovo_assemblies/Stats_raw_assemblies.tab
while read sample;
do
echo $sample;
python /home/alice/Common_scripts/Stats_from_fasta.py \
/data2/alice/WW_project/0_Data/2_Denovo_assemblies/${sample}/scaffolds.fasta;
cat /data2/alice/WW_project/0_Data/2_Denovo_assemblies/${sample}/scaffolds.fasta_stats.txt | \
awk -v sample=$sample 'BEGIN{FS = "\t"; OFS = "\t"} {print sample, "Raw", $1, $2} ' >> \
/data2/alice/WW_project/0_Data/2_Denovo_assemblies/Stats_raw_assemblies.tab ;
done < Keep_lists_samples/Assembled.sample_list.args
## 05STB001_1
## Number of contigs is 889. Cumulated length is 36.23Mb.
## 05STB003_1
## Number of contigs is 933. Cumulated length is 36.62Mb.
## 05STB011_1
## Number of contigs is 983. Cumulated length is 36.25Mb.
## 05STB012_1
## Number of contigs is 999. Cumulated length is 36.71Mb.
## 05STB013_1
## Number of contigs is 931. Cumulated length is 35.24Mb.
## 05STB015_1
## Number of contigs is 875. Cumulated length is 35.69Mb.
## 05STB017_1
## Number of contigs is 1310. Cumulated length is 38.01Mb.
## 05STB023_1
## Number of contigs is 868. Cumulated length is 35.99Mb.
## 05STB026_1
## Number of contigs is 896. Cumulated length is 36.77Mb.
## 05STB028_1
## Number of contigs is 885. Cumulated length is 35.77Mb.
## 05STCH001_1
## Number of contigs is 936. Cumulated length is 36.92Mb.
## 05STCH002_1
## Number of contigs is 759. Cumulated length is 34.85Mb.
## 05STCH003_1
## Number of contigs is 947. Cumulated length is 35.81Mb.
## 05STCH004_1
## Number of contigs is 1064. Cumulated length is 35.34Mb.
## 05STCH008_1
## Number of contigs is 913. Cumulated length is 35.48Mb.
## 05STD001_1
## Number of contigs is 1212. Cumulated length is 36.3Mb.
## 05STD006_1
## Number of contigs is 1005. Cumulated length is 36.22Mb.
## 05STD026_1
## Number of contigs is 786. Cumulated length is 34.57Mb.
## 05STD031_1
## Number of contigs is 943. Cumulated length is 36.31Mb.
## 05STD040_1
## Number of contigs is 874. Cumulated length is 36.33Mb.
## 05STD041_1
## Number of contigs is 824. Cumulated length is 36.05Mb.
## 05STD042_1
## Number of contigs is 956. Cumulated length is 36.88Mb.
## 05STD046_1
## Number of contigs is 917. Cumulated length is 34.52Mb.
## 05STD059_1
## Number of contigs is 893. Cumulated length is 36.51Mb.
## 05STD069_1
## Number of contigs is 884. Cumulated length is 36.21Mb.
## 05STD087_1
## Number of contigs is 987. Cumulated length is 35.93Mb.
## 05STD093_1
## Number of contigs is 815. Cumulated length is 35.5Mb.
## 05STD094_1
## Number of contigs is 897. Cumulated length is 36.03Mb.
## 05STD098_1
## Number of contigs is 923. Cumulated length is 35.69Mb.
## 05STD104_1
## Number of contigs is 787. Cumulated length is 35.63Mb.
## 05STD108_1
## Number of contigs is 945. Cumulated length is 36.98Mb.
## 05STD127_1
## Number of contigs is 859. Cumulated length is 35.83Mb.
## 05STD133_1
## Number of contigs is 950. Cumulated length is 36.13Mb.
## 05STD138_1
## Number of contigs is 933. Cumulated length is 36.35Mb.
## 05STIR001
## Number of contigs is 791. Cumulated length is 35.22Mb.
## 05STNL002_1
## Number of contigs is 740. Cumulated length is 36.14Mb.
## 05STNL003_1
## Number of contigs is 837. Cumulated length is 35.96Mb.
## 05STNL015_1
## Number of contigs is 967. Cumulated length is 36.51Mb.
## 05STNL024_1
## Number of contigs is 950. Cumulated length is 35.46Mb.
## 05STPL002_1
## Number of contigs is 858. Cumulated length is 35.3Mb.
## 05STPL003_1
## Number of contigs is 821. Cumulated length is 35.1Mb.
## 05STPL005_1
## Number of contigs is 1966. Cumulated length is 37.93Mb.
## 05STPL007_1
## Number of contigs is 857. Cumulated length is 36.7Mb.
## 05STPL008_1
## Number of contigs is 1388. Cumulated length is 37.07Mb.
## 06STCZ001
## Number of contigs is 1028. Cumulated length is 36.77Mb.
## 06STCZ003
## Number of contigs is 1004. Cumulated length is 35.79Mb.
## 06STCZ007
## Number of contigs is 1164. Cumulated length is 36.45Mb.
## 06STCZ009
## Number of contigs is 993. Cumulated length is 36.14Mb.
## 06STCZ016
## Number of contigs is 823. Cumulated length is 35.61Mb.
## 06STCZ020
## Number of contigs is 935. Cumulated length is 35.49Mb.
## 06STCZ023
## Number of contigs is 963. Cumulated length is 35.52Mb.
## 06STCZ028
## Number of contigs is 1043. Cumulated length is 35.55Mb.
## 06STCZ036
## Number of contigs is 1018. Cumulated length is 35.95Mb.
## 06STCZ044
## Number of contigs is 919. Cumulated length is 36.05Mb.
## 06STCZ045
## Number of contigs is 1059. Cumulated length is 36.58Mb.
## 06STD024
## Number of contigs is 1077. Cumulated length is 39.75Mb.
## 06STGB002
## Number of contigs is 944. Cumulated length is 36.01Mb.
## 06STGB003
## Number of contigs is 941. Cumulated length is 35.58Mb.
## 06STGB006
## Number of contigs is 789. Cumulated length is 35.7Mb.
## 06STGB013
## Number of contigs is 1003. Cumulated length is 36.31Mb.
## 06STGB015
## Number of contigs is 870. Cumulated length is 35.95Mb.
## 06STGB018
## Number of contigs is 947. Cumulated length is 35.88Mb.
## 06STGB020
## Number of contigs is 789. Cumulated length is 36.37Mb.
## 06STIR001
## Number of contigs is 912. Cumulated length is 36.03Mb.
## 06STIR002
## Number of contigs is 904. Cumulated length is 36.12Mb.
## 06STIR003
## Number of contigs is 785. Cumulated length is 32.6Mb.
## 06STIR004
## Number of contigs is 879. Cumulated length is 36.04Mb.
## 06STIR005
## Number of contigs is 882. Cumulated length is 35.89Mb.
## 06STIR008
## Number of contigs is 872. Cumulated length is 35.6Mb.
## 07STF011
## Number of contigs is 902. Cumulated length is 37.13Mb.
## 07STF021
## Number of contigs is 777. Cumulated length is 35.6Mb.
## 07STF031
## Number of contigs is 899. Cumulated length is 36.79Mb.
## 07STF041
## Number of contigs is 969. Cumulated length is 35.72Mb.
## 07STF051
## Number of contigs is 986. Cumulated length is 35.4Mb.
## 07STF058
## Number of contigs is 992. Cumulated length is 37.1Mb.
## 07STF094
## Number of contigs is 868. Cumulated length is 36.33Mb.
## 07STF104
## Number of contigs is 807. Cumulated length is 35.03Mb.
## 07STF145
## Number of contigs is 906. Cumulated length is 36.56Mb.
## 07STF146
## Number of contigs is 973. Cumulated length is 36.23Mb.
## 07STF148
## Number of contigs is 849. Cumulated length is 35.87Mb.
## 07STF160
## Number of contigs is 997. Cumulated length is 36.14Mb.
## 07STF190
## Number of contigs is 804. Cumulated length is 35.36Mb.
## 07STGB009
## Number of contigs is 621. Cumulated length is 35.71Mb.
## 08STB003
## Number of contigs is 892. Cumulated length is 35.91Mb.
## 08STB009
## Number of contigs is 903. Cumulated length is 35.1Mb.
## 08STB010
## Number of contigs is 854. Cumulated length is 35.63Mb.
## 08STB011
## Number of contigs is 871. Cumulated length is 34.09Mb.
## 08STCH005
## Number of contigs is 878. Cumulated length is 35.51Mb.
## 08STCH007
## Number of contigs is 893. Cumulated length is 36.46Mb.
## 08STCH008
## Number of contigs is 883. Cumulated length is 35.96Mb.
## 08STCH015
## Number of contigs is 858. Cumulated length is 36.81Mb.
## 08STCZ003
## Number of contigs is 1006. Cumulated length is 36.45Mb.
## 08STCZ004
## Number of contigs is 993. Cumulated length is 37.1Mb.
## 08STCZ010
## Number of contigs is 1031. Cumulated length is 36.56Mb.
## 08STCZ011
## Number of contigs is 1502. Cumulated length is 42.28Mb.
## 08STCZ015
## Number of contigs is 783. Cumulated length is 35.52Mb.
## 08STCZ016
## Number of contigs is 1040. Cumulated length is 36.65Mb.
## 08STCZ023
## Number of contigs is 933. Cumulated length is 36.01Mb.
## 08STD013
## Number of contigs is 984. Cumulated length is 35.57Mb.
## 08STD016
## Number of contigs is 835. Cumulated length is 36.05Mb.
## 08STD018
## Number of contigs is 878. Cumulated length is 36.24Mb.
## 08STD019
## Number of contigs is 1001. Cumulated length is 36.18Mb.
## 08STD020
## Number of contigs is 837. Cumulated length is 35.97Mb.
## 08STD021
## Number of contigs is 968. Cumulated length is 36.02Mb.
## 08STD022
## Number of contigs is 930. Cumulated length is 35.7Mb.
## 08STD045
## Number of contigs is 896. Cumulated length is 36.1Mb.
## 08STD046
## Number of contigs is 938. Cumulated length is 36.24Mb.
## 08STF006
## Number of contigs is 950. Cumulated length is 36.2Mb.
## 08STF029
## Number of contigs is 910. Cumulated length is 35.39Mb.
## 08STF030
## Number of contigs is 955. Cumulated length is 35.28Mb.
## 08STF034
## Number of contigs is 933. Cumulated length is 34.01Mb.
## 08STF035
## Number of contigs is 916. Cumulated length is 35.56Mb.
## 08STF036
## Number of contigs is 929. Cumulated length is 34.73Mb.
## 08STF040
## Number of contigs is 945. Cumulated length is 36.18Mb.
## 08STF048
## Number of contigs is 921. Cumulated length is 36.84Mb.
## 08STF051
## Number of contigs is 958. Cumulated length is 35.05Mb.
## 08STF052
## Number of contigs is 987. Cumulated length is 35.38Mb.
## 08STF056
## Number of contigs is 987. Cumulated length is 36.78Mb.
## 08STF063
## Number of contigs is 1018. Cumulated length is 36.99Mb.
## 08STF070
## Number of contigs is 962. Cumulated length is 35.51Mb.
## 08STF076
## Number of contigs is 961. Cumulated length is 35.82Mb.
## 08STF077
## Number of contigs is 940. Cumulated length is 35.74Mb.
## 08STF078
## Number of contigs is 873. Cumulated length is 36.6Mb.
## 08STF079
## Number of contigs is 938. Cumulated length is 35.96Mb.
## 08STF082
## Number of contigs is 906. Cumulated length is 35.65Mb.
## 08STF083
## Number of contigs is 1066. Cumulated length is 35.54Mb.
## 08STF089
## Number of contigs is 967. Cumulated length is 36.03Mb.
## 08STF094
## Number of contigs is 1048. Cumulated length is 36.44Mb.
## 08STF098
## Number of contigs is 829. Cumulated length is 36.0Mb.
## 08STF102
## Number of contigs is 1136. Cumulated length is 36.02Mb.
## 08STF105
## Number of contigs is 1012. Cumulated length is 35.52Mb.
## 08STF106
## Number of contigs is 893. Cumulated length is 35.57Mb.
## 08STF108
## Number of contigs is 780. Cumulated length is 34.05Mb.
## 08STF109
## Number of contigs is 908. Cumulated length is 34.69Mb.
## 08STF116
## Number of contigs is 986. Cumulated length is 35.44Mb.
## 08STF128
## Number of contigs is 861. Cumulated length is 35.51Mb.
## 08STF131
## Number of contigs is 950. Cumulated length is 35.29Mb.
## 08STF136
## Number of contigs is 916. Cumulated length is 34.5Mb.
## 08STF147
## Number of contigs is 932. Cumulated length is 34.84Mb.
## 08STF153
## Number of contigs is 1011. Cumulated length is 36.3Mb.
## 08STF155
## Number of contigs is 940. Cumulated length is 35.93Mb.
## 08STF175
## Number of contigs is 880. Cumulated length is 35.39Mb.
## 08STF183
## Number of contigs is 1012. Cumulated length is 36.38Mb.
## 08STF185
## Number of contigs is 1086. Cumulated length is 36.26Mb.
## 08STF187
## Number of contigs is 852. Cumulated length is 36.35Mb.
## 08STF194
## Number of contigs is 842. Cumulated length is 33.99Mb.
## 08STF196
## Number of contigs is 868. Cumulated length is 34.36Mb.
## 08STGB001
## Number of contigs is 825. Cumulated length is 35.5Mb.
## 08STGB003
## Number of contigs is 909. Cumulated length is 36.78Mb.
## 08STGB004
## Number of contigs is 836. Cumulated length is 36.22Mb.
## 08STGB006
## Number of contigs is 879. Cumulated length is 35.81Mb.
## 08STGB007
## Number of contigs is 881. Cumulated length is 36.6Mb.
## 09STD003
## Number of contigs is 711. Cumulated length is 37.19Mb.
## 09STD004
## Number of contigs is 744. Cumulated length is 36.98Mb.
## 09STD007
## Number of contigs is 651. Cumulated length is 36.78Mb.
## 09STD019
## Number of contigs is 971. Cumulated length is 35.85Mb.
## 09STD024
## Number of contigs is 734. Cumulated length is 38.0Mb.
## 09STD031
## Number of contigs is 735. Cumulated length is 36.6Mb.
## 09STD041
## Number of contigs is 737. Cumulated length is 37.44Mb.
## 09STD044
## Number of contigs is 646. Cumulated length is 37.89Mb.
## 09STD053
## Number of contigs is 847. Cumulated length is 37.29Mb.
## 09STD054
## Number of contigs is 881. Cumulated length is 36.68Mb.
## 09STD057
## Number of contigs is 574. Cumulated length is 35.53Mb.
## 09STD059
## Number of contigs is 712. Cumulated length is 36.75Mb.
## 09STD061
## Number of contigs is 916. Cumulated length is 36.01Mb.
## 09STD062
## Number of contigs is 760. Cumulated length is 37.16Mb.
## 09STD070
## Number of contigs is 735. Cumulated length is 36.47Mb.
## 09STD071
## Number of contigs is 978. Cumulated length is 36.31Mb.
## 09STD072
## Number of contigs is 1075. Cumulated length is 37.07Mb.
## 09STD073
## Number of contigs is 776. Cumulated length is 36.93Mb.
## 09STD074
## Number of contigs is 1226. Cumulated length is 34.9Mb.
## 09STD075
## Number of contigs is 1100. Cumulated length is 36.14Mb.
## 09STD076
## Number of contigs is 562. Cumulated length is 38.14Mb.
## 09STD077
## Number of contigs is 781. Cumulated length is 36.25Mb.
## 09STD078
## Number of contigs is 801. Cumulated length is 37.01Mb.
## 09STD079
## Number of contigs is 766. Cumulated length is 37.46Mb.
## 09STE001
## Number of contigs is 792. Cumulated length is 37.0Mb.
## 09STE002
## Number of contigs is 729. Cumulated length is 37.43Mb.
## 09STF004
## Number of contigs is 714. Cumulated length is 37.53Mb.
## 09STF005
## Number of contigs is 726. Cumulated length is 35.77Mb.
## 09STF007
## Number of contigs is 880. Cumulated length is 36.54Mb.
## 09STF011
## Number of contigs is 752. Cumulated length is 35.82Mb.
## 09STF013
## Number of contigs is 663. Cumulated length is 35.95Mb.
## 09STF014
## Number of contigs is 861. Cumulated length is 35.65Mb.
## 09STF015
## Number of contigs is 1084. Cumulated length is 36.26Mb.
## 09STF019
## Number of contigs is 1147. Cumulated length is 36.06Mb.
## 09STF024
## Number of contigs is 594. Cumulated length is 37.88Mb.
## 09STF025
## Number of contigs is 700. Cumulated length is 37.07Mb.
## 09STF027
## Number of contigs is 1129. Cumulated length is 41.23Mb.
## 09STF028
## Number of contigs is 1110. Cumulated length is 35.79Mb.
## 09STF029
## Number of contigs is 693. Cumulated length is 34.5Mb.
## 09STF031
## Number of contigs is 2598. Cumulated length is 38.7Mb.
## 09STF032
## Number of contigs is 3071. Cumulated length is 38.6Mb.
## 09STF036
## Number of contigs is 745. Cumulated length is 37.4Mb.
## 09STF037
## Number of contigs is 753. Cumulated length is 38.03Mb.
## 09STF045
## Number of contigs is 778. Cumulated length is 37.23Mb.
## 09STF046
## Number of contigs is 882. Cumulated length is 37.47Mb.
## 09STF048
## Number of contigs is 675. Cumulated length is 37.29Mb.
## 09STF054
## Number of contigs is 670. Cumulated length is 37.36Mb.
## 09STF056
## Number of contigs is 587. Cumulated length is 36.75Mb.
## 09STF058
## Number of contigs is 613. Cumulated length is 36.24Mb.
## 09STF063
## Number of contigs is 639. Cumulated length is 37.05Mb.
## 09STF068
## Number of contigs is 1539. Cumulated length is 37.91Mb.
## 09STF077
## Number of contigs is 940. Cumulated length is 36.71Mb.
## 09STF079
## Number of contigs is 879. Cumulated length is 36.51Mb.
## 09STF081
## Number of contigs is 622. Cumulated length is 36.14Mb.
## 09STF082
## Number of contigs is 855. Cumulated length is 36.84Mb.
## 09STF094
## Number of contigs is 753. Cumulated length is 35.67Mb.
## 09STF096
## Number of contigs is 641. Cumulated length is 37.0Mb.
## 09STF097
## Number of contigs is 599. Cumulated length is 36.64Mb.
## 09STF098
## Number of contigs is 623. Cumulated length is 37.29Mb.
## 09STF099
## Number of contigs is 663. Cumulated length is 36.8Mb.
## 09STF103
## Number of contigs is 883. Cumulated length is 37.79Mb.
## 09STF105
## Number of contigs is 538. Cumulated length is 36.15Mb.
## 09STF106
## Number of contigs is 630. Cumulated length is 37.49Mb.
## 09STF109
## Number of contigs is 893. Cumulated length is 36.32Mb.
## 09STF112
## Number of contigs is 976. Cumulated length is 37.14Mb.
## 09STF114
## Number of contigs is 791. Cumulated length is 37.01Mb.
## 09STGB001
## Number of contigs is 534. Cumulated length is 36.07Mb.
## 09STGB002
## Number of contigs is 874. Cumulated length is 36.36Mb.
## 09STGB004
## Number of contigs is 509. Cumulated length is 36.84Mb.
## 09STIR003_1
## Number of contigs is 806. Cumulated length is 37.32Mb.
## 09STIR004_2
## Number of contigs is 807. Cumulated length is 36.42Mb.
## 09STIR005_2
## Number of contigs is 732. Cumulated length is 36.61Mb.
## 09STIR007_3
## Number of contigs is 575. Cumulated length is 37.2Mb.
## 09STIR009_5
## Number of contigs is 941. Cumulated length is 36.32Mb.
## 09STIR010_4
## Number of contigs is 535. Cumulated length is 37.65Mb.
## 09STIR012_3
## Number of contigs is 594. Cumulated length is 36.58Mb.
## 09STIR013_1
## Number of contigs is 567. Cumulated length is 35.42Mb.
## 09STIR014_1
## Number of contigs is 788. Cumulated length is 38.0Mb.
## 09STIR014_3
## Number of contigs is 957. Cumulated length is 36.37Mb.
## 09STIR015_1
## Number of contigs is 662. Cumulated length is 33.94Mb.
## 09STIR016_2
## Number of contigs is 854. Cumulated length is 36.16Mb.
## 09STIR016_3
## Number of contigs is 794. Cumulated length is 36.07Mb.
## 09STIR017_5
## Number of contigs is 686. Cumulated length is 36.83Mb.
## 09STIR018_1
## Number of contigs is 723. Cumulated length is 37.22Mb.
## 09STIR019_4
## Number of contigs is 873. Cumulated length is 37.32Mb.
## 09STIR020_1
## Number of contigs is 657. Cumulated length is 36.88Mb.
## 09STIR020_3
## Number of contigs is 585. Cumulated length is 37.32Mb.
## 09STIR021_2
## Number of contigs is 787. Cumulated length is 37.16Mb.
## 09STIR022_1
## Number of contigs is 634. Cumulated length is 37.19Mb.
## 09STIR022_4
## Number of contigs is 786. Cumulated length is 37.67Mb.
## 09STIR023_3
## Number of contigs is 749. Cumulated length is 37.07Mb.
## 09STIR024_2
## Number of contigs is 704. Cumulated length is 37.11Mb.
## 09STIR026_2
## Number of contigs is 3833. Cumulated length is 39.97Mb.
## 09STIR026_4
## Number of contigs is 538. Cumulated length is 35.64Mb.
## 09STIR026_5
## Number of contigs is 550. Cumulated length is 35.51Mb.
## 09STIR027_3
## Number of contigs is 537. Cumulated length is 35.75Mb.
## 09STIR027_5
## Number of contigs is 996. Cumulated length is 36.23Mb.
## 10STBY001
## Number of contigs is 812. Cumulated length is 34.72Mb.
## 10STD001
## Number of contigs is 1085. Cumulated length is 36.32Mb.
## 10STD002
## Number of contigs is 864. Cumulated length is 39.54Mb.
## 10STD017
## Number of contigs is 862. Cumulated length is 35.2Mb.
## 10STD019
## Number of contigs is 956. Cumulated length is 36.68Mb.
## 10STDK003
## Number of contigs is 872. Cumulated length is 35.9Mb.
## 10STF023
## Number of contigs is 836. Cumulated length is 34.83Mb.
## 10STF036
## Number of contigs is 911. Cumulated length is 34.9Mb.
## 10STF049
## Number of contigs is 944. Cumulated length is 35.76Mb.
## 10STF057
## Number of contigs is 943. Cumulated length is 36.49Mb.
## 10STF058
## Number of contigs is 884. Cumulated length is 35.97Mb.
## 10STF078
## Number of contigs is 935. Cumulated length is 36.57Mb.
## 10STF082
## Number of contigs is 1020. Cumulated length is 36.2Mb.
## 10STF146
## Number of contigs is 908. Cumulated length is 36.06Mb.
## 10STF150
## Number of contigs is 904. Cumulated length is 35.86Mb.
## 10STF163
## Number of contigs is 1027. Cumulated length is 35.53Mb.
## 10STF164
## Number of contigs is 915. Cumulated length is 36.05Mb.
## 10STF178
## Number of contigs is 994. Cumulated length is 36.86Mb.
## 10STF190
## Number of contigs is 873. Cumulated length is 36.73Mb.
## 10STF202
## Number of contigs is 1011. Cumulated length is 35.8Mb.
## 10STF227
## Number of contigs is 894. Cumulated length is 36.36Mb.
## 10STF231
## Number of contigs is 973. Cumulated length is 36.3Mb.
## 10STF241
## Number of contigs is 846. Cumulated length is 36.26Mb.
## 10STF248
## Number of contigs is 779. Cumulated length is 35.03Mb.
## 10STF253
## Number of contigs is 961. Cumulated length is 35.54Mb.
## 10STF261
## Number of contigs is 985. Cumulated length is 36.33Mb.
## 10STGB007
## Number of contigs is 1092. Cumulated length is 35.92Mb.
## 10STGB015
## Number of contigs is 837. Cumulated length is 35.97Mb.
## 10STGB024
## Number of contigs is 908. Cumulated length is 36.2Mb.
## 10STGB025
## Number of contigs is 947. Cumulated length is 35.67Mb.
## 10STGB031
## Number of contigs is 723. Cumulated length is 34.42Mb.
## 10STGB035
## Number of contigs is 877. Cumulated length is 34.86Mb.
## 10STGB036
## Number of contigs is 943. Cumulated length is 36.34Mb.
## 10STGB037
## Number of contigs is 855. Cumulated length is 33.63Mb.
## 10ST_Syn_D003
## Number of contigs is 897. Cumulated length is 35.95Mb.
## 10ST_Syn_D005
## Number of contigs is 977. Cumulated length is 35.72Mb.
## Algeria_1992_ALA1c
## Number of contigs is 1176. Cumulated length is 35.0Mb.
## Algeria_1992_ALA2a
## Number of contigs is 851. Cumulated length is 35.1Mb.
## Algeria_1992_ALA3a
## Number of contigs is 1445. Cumulated length is 35.09Mb.
## Algeria_1992_ALG1a
## Number of contigs is 1450. Cumulated length is 35.15Mb.
## Algeria_1992_ALG1d
## Number of contigs is 1248. Cumulated length is 35.18Mb.
## Algeria_1992_ALG1e
## Number of contigs is 1332. Cumulated length is 35.76Mb.
## Argentina_2000_BOO10_F9a2
## Number of contigs is 1366. Cumulated length is 36.42Mb.
## Argentina_2000_BOO12_F5a1
## Number of contigs is 1211. Cumulated length is 36.64Mb.
## Argentina_2000_BOO14_F15a3
## Number of contigs is 1246. Cumulated length is 36.31Mb.
## Argentina_2000_BOO28_F15b2
## Number of contigs is 1676. Cumulated length is 37.09Mb.
## Argentina_2000_BOO32_B5a1
## Number of contigs is 1063. Cumulated length is 36.73Mb.
## Argentina_2000_BOO36_B4a1
## Number of contigs is 1378. Cumulated length is 36.91Mb.
## Argentina_2000_BOO54_F8b1
## Number of contigs is 1147. Cumulated length is 34.77Mb.
## Argentina_2000_BOO59_C4a2
## Number of contigs is 1037. Cumulated length is 36.01Mb.
## Argentina_2000_BOO61_FI5b2p
## Number of contigs is 947. Cumulated length is 36.69Mb.
## Argentina_2000_BOO71_EI1a2p
## Number of contigs is 1732. Cumulated length is 36.92Mb.
## Argentina_2000_BOO9_F15a2
## Number of contigs is 1135. Cumulated length is 36.13Mb.
## California_1989_CB11A_ST1
## Number of contigs is 1224. Cumulated length is 35.19Mb.
## California_1989_CC22C_ST16
## Number of contigs is 1227. Cumulated length is 35.76Mb.
## California_1989_CE31B_ST42
## Number of contigs is 1626. Cumulated length is 36.57Mb.
## California_1989_CF11A_ST44
## Number of contigs is 1181. Cumulated length is 35.28Mb.
## California_1989_CF31C_ST52
## Number of contigs is 1231. Cumulated length is 35.14Mb.
## California_1989_CH33C_ST97
## Number of contigs is 1095. Cumulated length is 35.33Mb.
## Canada_1992_CNRA1a_1
## Number of contigs is 2030. Cumulated length is 36.87Mb.
## Canada_1992_CNRA4b_1
## Number of contigs is 1267. Cumulated length is 35.56Mb.
## Canada_1992_CNRB2b_4
## Number of contigs is 1816. Cumulated length is 33.5Mb.
## Canada_1992_CNRD4a_2
## Number of contigs is 1522. Cumulated length is 35.7Mb.
## Canada_1992_CNRE2a_2
## Number of contigs is 1358. Cumulated length is 35.69Mb.
## Canada_1992_CNRE4b_1
## Number of contigs is 1649. Cumulated length is 35.9Mb.
## Canada_1992_CNRG3a_1
## Number of contigs is 1399. Cumulated length is 36.29Mb.
## Canada_1992_CNRH3a_1
## Number of contigs is 1330. Cumulated length is 35.7Mb.
## Chile_1995_STCH95_10B4a
## Number of contigs is 1279. Cumulated length is 34.48Mb.
## Chile_1995_STCH95_1A2a
## Number of contigs is 1150. Cumulated length is 35.02Mb.
## Chile_1995_STCH95_1B1a
## Number of contigs is 1382. Cumulated length is 35.05Mb.
## Chile_1995_STCH95_1B2a
## Number of contigs is 1244. Cumulated length is 34.72Mb.
## Chile_1995_STCH95_1C3a
## Number of contigs is 1253. Cumulated length is 35.19Mb.
## Chile_1995_STCH95_1F2a
## Number of contigs is 1028. Cumulated length is 32.97Mb.
## Chile_1995_STCH95_1F3a
## Number of contigs is 1081. Cumulated length is 34.19Mb.
## Chile_1995_STCH95_1G3a
## Number of contigs is 1073. Cumulated length is 35.13Mb.
## Chile_1995_STCH95_1H1a
## Number of contigs is 1263. Cumulated length is 34.96Mb.
## Chile_1995_STCH95_1H2a
## Number of contigs is 1388. Cumulated length is 35.51Mb.
## Chile_1995_STCH95_3A3a
## Number of contigs is 1212. Cumulated length is 36.07Mb.
## Chile_1995_STCH95_3E4a
## Number of contigs is 1196. Cumulated length is 36.11Mb.
## Ethiopia_1992_ETD1
## Number of contigs is 1165. Cumulated length is 34.67Mb.
## Ethiopia_1992_ETK1
## Number of contigs is 1181. Cumulated length is 35.68Mb.
## Ethiopia_1992_ETK2a_1
## Number of contigs is 1216. Cumulated length is 35.48Mb.
## Ethiopia_1992_ETK2a_2
## Number of contigs is 1439. Cumulated length is 35.73Mb.
## Indiana_1993_I15a_1
## Number of contigs is 1298. Cumulated length is 36.1Mb.
## Indiana_1993_I1a_1
## Number of contigs is 1529. Cumulated length is 35.54Mb.
## Indiana_1993_I22a_1
## Number of contigs is 1246. Cumulated length is 35.87Mb.
## Indiana_1993_I24a_1
## Number of contigs is 1174. Cumulated length is 36.13Mb.
## Indiana_1993_I25a_1
## Number of contigs is 1050. Cumulated length is 35.78Mb.
## Indiana_1993_I31a_1
## Number of contigs is 1098. Cumulated length is 35.64Mb.
## Indiana_1993_I33a_1
## Number of contigs is 1098. Cumulated length is 35.35Mb.
## Indiana_1993_I9a_1
## Number of contigs is 1149. Cumulated length is 35.84Mb.
## Iran_2001_STIR01A13a
## Number of contigs is 1124. Cumulated length is 35.79Mb.
## Iran_2001_STIR01A18b
## Number of contigs is 914. Cumulated length is 35.57Mb.
## Iran_2001_STIR01A28a
## Number of contigs is 1073. Cumulated length is 35.81Mb.
## Iran_2001_STIR01A32a
## Number of contigs is 1000. Cumulated length is 36.15Mb.
## Iran_2001_STIR01A37a
## Number of contigs is 798. Cumulated length is 34.17Mb.
## Iran_2001_STIR01A44a
## Number of contigs is 824. Cumulated length is 34.03Mb.
## Iran_2001_STIR01A48b
## Number of contigs is 698. Cumulated length is 34.42Mb.
## Iran_2001_STIR01A78b
## Number of contigs is 763. Cumulated length is 34.59Mb.
## Iran_2001_STIR01A97a
## Number of contigs is 788. Cumulated length is 34.22Mb.
## Iran_2001_STIR01B74a
## Number of contigs is 778. Cumulated length is 34.97Mb.
## Iran_2001_STIR01B74b
## Number of contigs is 785. Cumulated length is 35.01Mb.
## Iran_2001_STIR01B76a
## Number of contigs is 905. Cumulated length is 35.95Mb.
## Iran_2001_STIR01B78a
## Number of contigs is 743. Cumulated length is 34.47Mb.
## Iran_2001_STIR01B83b
## Number of contigs is 840. Cumulated length is 34.66Mb.
## Israel_1992_ISYB1b
## Number of contigs is 884. Cumulated length is 36.11Mb.
## Israel_1992_ISYD3a_1
## Number of contigs is 840. Cumulated length is 34.83Mb.
## Israel_1992_ISYH1a
## Number of contigs is 1275. Cumulated length is 34.85Mb.
## Israel_1992_ISZA1c
## Number of contigs is 1081. Cumulated length is 35.26Mb.
## Israel_1992_ISZB3a_1
## Number of contigs is 1090. Cumulated length is 36.1Mb.
## Israel_1992_ISZC1a
## Number of contigs is 1047. Cumulated length is 35.77Mb.
## Israel_1992_ISZC2a_2
## Number of contigs is 917. Cumulated length is 35.71Mb.
## Israel_1992_ISZE1b_2
## Number of contigs is 1141. Cumulated length is 34.35Mb.
## Israel_1992_ISZF2a_1
## Number of contigs is 965. Cumulated length is 34.97Mb.
## Israel_1992_ISZH2a
## Number of contigs is 1179. Cumulated length is 36.2Mb.
## Israel_1993_ISXBetC2a_1
## Number of contigs is 1074. Cumulated length is 36.46Mb.
## Israel_1993_ISXBetD4a_1
## Number of contigs is 992. Cumulated length is 35.73Mb.
## Israel_1993_ISXBetH3a_4
## Number of contigs is 930. Cumulated length is 35.4Mb.
## Kenya_1994_STKE94MF1a
## Number of contigs is 939. Cumulated length is 35.36Mb.
## Kenya_1994_STKE94MI1a
## Number of contigs is 1003. Cumulated length is 35.55Mb.
## Kenya_1994_STKE94ML1a
## Number of contigs is 1018. Cumulated length is 36.46Mb.
## Missouri_1994_ST94MO12a_1
## Number of contigs is 1025. Cumulated length is 35.7Mb.
## Missouri_1994_ST94MO15a_1
## Number of contigs is 1170. Cumulated length is 35.9Mb.
## Missouri_1994_ST94MO17a_1
## Number of contigs is 2477. Cumulated length is 37.15Mb.
## Missouri_1994_ST94MO19a_1
## Number of contigs is 1118. Cumulated length is 36.22Mb.
## Missouri_1994_ST94MO24a_1
## Number of contigs is 1362. Cumulated length is 35.68Mb.
## Missouri_1994_ST94MO2a_1
## Number of contigs is 1259. Cumulated length is 35.8Mb.
## Missouri_1994_ST94MO33a_1
## Number of contigs is 1189. Cumulated length is 35.35Mb.
## Missouri_1994_ST94MO35a_1
## Number of contigs is 1014. Cumulated length is 35.87Mb.
## Missouri_1994_ST94MO8a_1
## Number of contigs is 1105. Cumulated length is 35.95Mb.
## Missouri_1994_ST94Mo31a_1
## Number of contigs is 1343. Cumulated length is 35.99Mb.
## NTC_1
## Number of contigs is 0. Cumulated length is 0.0Mb.
## Traceback (most recent call last):
## File "/home/alice/Common_scripts/Stats_from_fasta.py", line 78, in <module>
## out.write(f"Smallest contig length\t{length_list[-1]}\n")
## IndexError: list index out of range
## NTC_2
## Number of contigs is 21. Cumulated length is 0.04Mb.
## ST00ARG_BD0069
## Number of contigs is 1001. Cumulated length is 33.12Mb.
## ST00ARG_BD1D1a1
## Number of contigs is 1321. Cumulated length is 33.3Mb.
## ST01AUS_1A4
## Number of contigs is 1123. Cumulated length is 32.16Mb.
## ST01AUS_1A5
## Number of contigs is 1162. Cumulated length is 32.44Mb.
## ST01AUS_1A6
## Number of contigs is 1259. Cumulated length is 33.07Mb.
## ST01AUS_1A9
## Number of contigs is 1155. Cumulated length is 32.67Mb.
## ST01AUS_1B1
## Number of contigs is 1148. Cumulated length is 32.62Mb.
## ST01AUS_1B2
## Number of contigs is 1136. Cumulated length is 32.08Mb.
## ST01AUS_1B7
## Number of contigs is 1142. Cumulated length is 32.97Mb.
## ST01AUS_1B8
## Number of contigs is 1207. Cumulated length is 32.99Mb.
## ST01AUS_1C1
## Number of contigs is 1197. Cumulated length is 32.6Mb.
## ST01AUS_1C2
## Number of contigs is 1212. Cumulated length is 32.47Mb.
## ST01AUS_1C3
## Number of contigs is 1141. Cumulated length is 32.61Mb.
## ST01AUS_1C6
## Number of contigs is 1057. Cumulated length is 31.16Mb.
## ST01AUS_1C8
## Number of contigs is 1038. Cumulated length is 31.72Mb.
## ST01AUS_1D4
## Number of contigs is 1202. Cumulated length is 32.67Mb.
## ST01AUS_1D5
## Number of contigs is 1257. Cumulated length is 32.94Mb.
## ST01AUS_1D8
## Number of contigs is 1162. Cumulated length is 32.68Mb.
## ST01AUS_1E1
## Number of contigs is 1146. Cumulated length is 31.28Mb.
## ST01AUS_1E4
## Number of contigs is 1176. Cumulated length is 31.51Mb.
## ST01AUS_1E5
## Number of contigs is 1183. Cumulated length is 32.72Mb.
## ST01AUS_1F2
## Number of contigs is 1115. Cumulated length is 32.68Mb.
## ST01AUS_1F3
## Number of contigs is 1250. Cumulated length is 32.7Mb.
## ST01AUS_1F8
## Number of contigs is 1199. Cumulated length is 32.42Mb.
## ST01AUS_1G2
## Number of contigs is 1118. Cumulated length is 32.06Mb.
## ST01AUS_1G5
## Number of contigs is 1189. Cumulated length is 33.04Mb.
## ST01AUS_1H2
## Number of contigs is 1210. Cumulated length is 32.91Mb.
## ST01AUS_1H6
## Number of contigs is 1205. Cumulated length is 32.96Mb.
## ST01AUS_1H8
## Number of contigs is 1162. Cumulated length is 32.55Mb.
## ST05DK_01B5
## Number of contigs is 840. Cumulated length is 33.42Mb.
## ST05DK_01a1
## Number of contigs is 944. Cumulated length is 33.73Mb.
## ST05DK_01a4
## Number of contigs is 896. Cumulated length is 33.01Mb.
## ST05DK_01ab1
## Number of contigs is 1285. Cumulated length is 32.54Mb.
## ST06FR_Biog_G84
## Number of contigs is 973. Cumulated length is 34.3Mb.
## ST07SP_Biog_G85
## Number of contigs is 3140. Cumulated length is 33.08Mb.
## ST08TN_26_5_4
## Number of contigs is 938. Cumulated length is 33.72Mb.
## ST09FR_Biog_G01
## Number of contigs is 9381. Cumulated length is 26.06Mb.
## ST09FR_Biog_G02
## Number of contigs is 1178. Cumulated length is 33.16Mb.
## ST09FR_Biog_G03
## Number of contigs is 1607. Cumulated length is 34.57Mb.
## ST09FR_Biog_G04
## Number of contigs is 1519. Cumulated length is 34.28Mb.
## ST09FR_Biog_G05
## Number of contigs is 2380. Cumulated length is 34.02Mb.
## ST09FR_Biog_G06
## Number of contigs is 1886. Cumulated length is 33.46Mb.
## ST09FR_Biog_G07
## Number of contigs is 1178. Cumulated length is 34.03Mb.
## ST09FR_Biog_G08
## Number of contigs is 1830. Cumulated length is 33.56Mb.
## ST09FR_Biog_G09
## Number of contigs is 1220. Cumulated length is 33.71Mb.
## ST09FR_Biog_G10
## Number of contigs is 1123. Cumulated length is 34.02Mb.
## ST09FR_Biog_G11
## Number of contigs is 1516. Cumulated length is 34.18Mb.
## ST09FR_Biog_G12
## Number of contigs is 1611. Cumulated length is 34.67Mb.
## ST09FR_Biog_G13
## Number of contigs is 3603. Cumulated length is 34.32Mb.
## ST09FR_Biog_G14
## Number of contigs is 3732. Cumulated length is 34.59Mb.
## ST09FR_Biog_G15
## Number of contigs is 2180. Cumulated length is 32.99Mb.
## ST09FR_Biog_G16
## Number of contigs is 1301. Cumulated length is 34.77Mb.
## ST09FR_Biog_G17
## Number of contigs is 1282. Cumulated length is 34.19Mb.
## ST09FR_Biog_G18
## Number of contigs is 1280. Cumulated length is 34.98Mb.
## ST09FR_Biog_G19
## Number of contigs is 1388. Cumulated length is 34.83Mb.
## ST09FR_Biog_G20
## Number of contigs is 2814. Cumulated length is 34.0Mb.
## ST09FR_Biog_G21
## Number of contigs is 4731. Cumulated length is 33.46Mb.
## ST09FR_Biog_G22
## Number of contigs is 2217. Cumulated length is 32.43Mb.
## ST09FR_Biog_G23
## Number of contigs is 1159. Cumulated length is 36.13Mb.
## ST09FR_Biog_G24
## Number of contigs is 1521. Cumulated length is 33.37Mb.
## ST09FR_Biog_G25
## Number of contigs is 1352. Cumulated length is 33.95Mb.
## ST09FR_Biog_G26
## Number of contigs is 1400. Cumulated length is 34.04Mb.
## ST09FR_Biog_G27
## Number of contigs is 1611. Cumulated length is 34.33Mb.
## ST09FR_Biog_G28
## Number of contigs is 1828. Cumulated length is 34.48Mb.
## ST09FR_Biog_G29
## Number of contigs is 5090. Cumulated length is 34.03Mb.
## ST09FR_Biog_G30
## Number of contigs is 3100. Cumulated length is 34.85Mb.
## ST09FR_Biog_G31
## Number of contigs is 1769. Cumulated length is 34.9Mb.
## ST09FR_Biog_G32
## Number of contigs is 1276. Cumulated length is 36.41Mb.
## ST09FR_Biog_G33
## Number of contigs is 1303. Cumulated length is 35.45Mb.
## ST09FR_Biog_G34
## Number of contigs is 1359. Cumulated length is 35.23Mb.
## ST09FR_Biog_G35
## Number of contigs is 1037. Cumulated length is 34.43Mb.
## ST09FR_Biog_G36
## Number of contigs is 2141. Cumulated length is 33.84Mb.
## ST09FR_Biog_G37
## Number of contigs is 4069. Cumulated length is 34.17Mb.
## ST09FR_Biog_G38
## Number of contigs is 775. Cumulated length is 35.81Mb.
## ST09FR_Biog_G39
## Number of contigs is 1351. Cumulated length is 34.13Mb.
## ST09FR_Biog_G40
## Number of contigs is 1369. Cumulated length is 35.62Mb.
## ST09FR_Biog_G41
## Number of contigs is 1409. Cumulated length is 35.62Mb.
## ST09FR_Biog_G42
## Number of contigs is 1264. Cumulated length is 35.34Mb.
## ST09FR_Biog_G43
## Number of contigs is 1285. Cumulated length is 35.22Mb.
## ST09FR_Biog_G44
## Number of contigs is 1462. Cumulated length is 35.48Mb.
## ST09FR_Biog_G45
## Number of contigs is 3136. Cumulated length is 34.75Mb.
## ST09FR_Biog_G46
## Number of contigs is 849. Cumulated length is 35.52Mb.
## ST09FR_Biog_G47
## Number of contigs is 1217. Cumulated length is 34.39Mb.
## ST09FR_Biog_G48
## Number of contigs is 1297. Cumulated length is 35.25Mb.
## ST09FR_Biog_G49
## Number of contigs is 1189. Cumulated length is 33.96Mb.
## ST09FR_Biog_G50
## Number of contigs is 1167. Cumulated length is 33.42Mb.
## ST09FR_Biog_G51
## Number of contigs is 1067. Cumulated length is 34.08Mb.
## ST09FR_Biog_G52
## Number of contigs is 1324. Cumulated length is 35.07Mb.
## ST09FR_Biog_G53
## Number of contigs is 3207. Cumulated length is 33.93Mb.
## ST09FR_Biog_G54
## Number of contigs is 1993. Cumulated length is 34.56Mb.
## ST09FR_Biog_G55
## Number of contigs is 2353. Cumulated length is 33.57Mb.
## ST09FR_Biog_G56
## Number of contigs is 1378. Cumulated length is 35.27Mb.
## ST09FR_Biog_G57
## Number of contigs is 1311. Cumulated length is 38.39Mb.
## ST09FR_Biog_G58
## Number of contigs is 1182. Cumulated length is 34.42Mb.
## ST09FR_Biog_G59
## Number of contigs is 1206. Cumulated length is 34.8Mb.
## ST09FR_Biog_G60
## Number of contigs is 1439. Cumulated length is 34.72Mb.
## ST09FR_Biog_G79
## Number of contigs is 1065. Cumulated length is 34.09Mb.
## ST09FR_Biog_G80
## Number of contigs is 905. Cumulated length is 34.37Mb.
## ST09FR_Biog_G82
## Number of contigs is 982. Cumulated length is 32.77Mb.
## ST09FR_Biog_I03
## Number of contigs is 735. Cumulated length is 33.79Mb.
## ST09FR_Biog_I04
## Number of contigs is 879. Cumulated length is 35.69Mb.
## ST09FR_Biog_I05
## Number of contigs is 794. Cumulated length is 34.23Mb.
## ST09FR_Biog_I07
## Number of contigs is 841. Cumulated length is 34.75Mb.
## ST09FR_Biog_I12
## Number of contigs is 869. Cumulated length is 35.06Mb.
## ST09FR_Biog_I24
## Number of contigs is 829. Cumulated length is 34.83Mb.
## ST09FR_Biog_I25
## Number of contigs is 864. Cumulated length is 34.57Mb.
## ST09FR_Biog_I28
## Number of contigs is 727. Cumulated length is 32.69Mb.
## ST10CRI_0450
## Number of contigs is 1386. Cumulated length is 33.21Mb.
## ST10CRI_0616
## Number of contigs is 854. Cumulated length is 33.31Mb.
## ST10FR_Biog_G093
## Number of contigs is 834. Cumulated length is 34.28Mb.
## ST10FR_Biog_G098
## Number of contigs is 918. Cumulated length is 35.32Mb.
## ST10FR_Biog_G100
## Number of contigs is 780. Cumulated length is 34.04Mb.
## ST10FR_Biog_G101
## Number of contigs is 831. Cumulated length is 34.55Mb.
## ST10FR_Biog_G102
## Number of contigs is 862. Cumulated length is 34.5Mb.
## ST10FR_Biog_G103
## Number of contigs is 840. Cumulated length is 34.45Mb.
## ST10FR_Biog_G61
## Number of contigs is 1566. Cumulated length is 34.49Mb.
## ST10FR_Biog_G62
## Number of contigs is 2203. Cumulated length is 35.26Mb.
## ST10FR_Biog_G63
## Number of contigs is 1827. Cumulated length is 34.27Mb.
## ST10FR_Biog_G64
## Number of contigs is 1360. Cumulated length is 34.8Mb.
## ST10FR_Biog_G65
## Number of contigs is 1279. Cumulated length is 33.98Mb.
## ST10FR_Biog_G66
## Number of contigs is 1255. Cumulated length is 35.14Mb.
## ST10FR_Biog_G67
## Number of contigs is 1325. Cumulated length is 35.27Mb.
## ST10FR_Biog_G68
## Number of contigs is 1613. Cumulated length is 34.57Mb.
## ST10FR_Biog_G69
## Number of contigs is 2113. Cumulated length is 34.36Mb.
## ST10FR_Biog_G70
## Number of contigs is 2898. Cumulated length is 34.21Mb.
## ST10FR_Biog_G73
## Number of contigs is 1120. Cumulated length is 33.31Mb.
## ST10FR_Biog_G74
## Number of contigs is 1279. Cumulated length is 34.99Mb.
## ST10FR_Biog_G83
## Number of contigs is 868. Cumulated length is 35.27Mb.
## ST10FR_Biog_G87
## Number of contigs is 871. Cumulated length is 35.22Mb.
## ST10FR_Biog_G88
## Number of contigs is 884. Cumulated length is 35.24Mb.
## ST10FR_Biog_G89
## Number of contigs is 842. Cumulated length is 34.06Mb.
## ST10FR_Biog_G90
## Number of contigs is 826. Cumulated length is 34.03Mb.
## ST10FR_Biog_G91
## Number of contigs is 865. Cumulated length is 35.13Mb.
## ST10FR_Biog_G92
## Number of contigs is 785. Cumulated length is 34.31Mb.
## ST10FR_Biog_G94
## Number of contigs is 785. Cumulated length is 33.9Mb.
## ST10FR_Biog_G95
## Number of contigs is 818. Cumulated length is 34.4Mb.
## ST10FR_Biog_G96
## Number of contigs is 765. Cumulated length is 34.14Mb.
## ST10FR_Biog_G97
## Number of contigs is 866. Cumulated length is 34.85Mb.
## ST10FR_Biog_G99
## Number of contigs is 847. Cumulated length is 35.02Mb.
## ST13FR_Biog_LG0595
## Number of contigs is 832. Cumulated length is 34.68Mb.
## ST13FR_Biog_SeptoDur10
## Number of contigs is 1187. Cumulated length is 34.52Mb.
## ST13FR_Biog_SeptoDur12
## Number of contigs is 1325. Cumulated length is 34.63Mb.
## ST13FR_Biog_SeptoDur29
## Number of contigs is 1195. Cumulated length is 34.36Mb.
## ST13FR_Biog_SeptoDur8
## Number of contigs is 1117. Cumulated length is 34.37Mb.
## ST13FR_Biog_SeptoDur82
## Number of contigs is 881. Cumulated length is 34.97Mb.
## ST13FR_Biog_SeptoDur88
## Number of contigs is 890. Cumulated length is 34.54Mb.
## ST13IT_Biog_1819
## Number of contigs is 848. Cumulated length is 33.11Mb.
## ST13IT_Biog_1863
## Number of contigs is 1173. Cumulated length is 33.23Mb.
## ST13NZ_St13_4_1
## Number of contigs is 1064. Cumulated length is 34.36Mb.
## ST13NZ_St13_4_2
## Number of contigs is 1007. Cumulated length is 34.22Mb.
## ST13NZ_St13_4_3
## Number of contigs is 1088. Cumulated length is 34.22Mb.
## ST13NZ_St13_5_1
## Number of contigs is 1197. Cumulated length is 33.61Mb.
## ST13NZ_St13_5_2
## Number of contigs is 1313. Cumulated length is 34.39Mb.
## ST13NZ_St13_5_3
## Number of contigs is 1166. Cumulated length is 33.68Mb.
## ST13NZ_St13_5_4
## Number of contigs is 1103. Cumulated length is 33.76Mb.
## ST13NZ_St13_6_1
## Number of contigs is 1257. Cumulated length is 33.47Mb.
## ST13NZ_St13_6_2
## Number of contigs is 1226. Cumulated length is 33.64Mb.
## ST13NZ_St13_6_3
## Number of contigs is 1135. Cumulated length is 33.37Mb.
## ST13NZ_St13_6_4
## Number of contigs is 1156. Cumulated length is 33.45Mb.
## ST13NZ_St13_7_1
## Number of contigs is 1181. Cumulated length is 33.36Mb.
## ST13NZ_St13_7_2
## Number of contigs is 1273. Cumulated length is 33.73Mb.
## ST13NZ_St13_7_3
## Number of contigs is 1192. Cumulated length is 33.49Mb.
## ST13NZ_St13_7_4
## Number of contigs is 1221. Cumulated length is 33.51Mb.
## ST13NZ_St13_8_1
## Number of contigs is 1287. Cumulated length is 33.86Mb.
## ST13NZ_St13_8_2
## Number of contigs is 1117. Cumulated length is 33.81Mb.
## ST13NZ_St13_8_3
## Number of contigs is 1153. Cumulated length is 34.01Mb.
## ST13NZ_St13_8_4
## Number of contigs is 1123. Cumulated length is 33.37Mb.
## ST13NZ_St13_9_1
## Number of contigs is 1178. Cumulated length is 33.19Mb.
## ST13NZ_St13_9_2
## Number of contigs is 1181. Cumulated length is 33.14Mb.
## ST13NZ_St13_9_3
## Number of contigs is 1150. Cumulated length is 34.05Mb.
## ST13NZ_St13_9_4
## Number of contigs is 1084. Cumulated length is 33.54Mb.
## ST13SP_Biog_SeptoDur104
## Number of contigs is 916. Cumulated length is 34.34Mb.
## ST14TAS_WAI1820
## Number of contigs is 1661. Cumulated length is 33.38Mb.
## ST14TAS_WAI1822
## Number of contigs is 1405. Cumulated length is 33.28Mb.
## ST14TAS_WAI1848
## Number of contigs is 1328. Cumulated length is 33.53Mb.
## ST14TAS_WAI1849
## Number of contigs is 1432. Cumulated length is 34.03Mb.
## ST14TAS_WAI1850
## Number of contigs is 1043. Cumulated length is 33.85Mb.
## ST14TAS_WAI1851
## Number of contigs is 1407. Cumulated length is 33.79Mb.
## ST14TAS_WAI1852
## Number of contigs is 1161. Cumulated length is 33.77Mb.
## ST14TAS_WAI1857
## Number of contigs is 251. Cumulated length is 0.58Mb.
## ST14TAS_WAI1858
## Number of contigs is 1256. Cumulated length is 33.44Mb.
## ST14TAS_WAI1859
## Number of contigs is 1722. Cumulated length is 33.47Mb.
## ST14TAS_WAI1875
## Number of contigs is 1237. Cumulated length is 33.67Mb.
## ST14TAS_WAI1876
## Number of contigs is 1208. Cumulated length is 33.87Mb.
## ST14TAS_WAI1877
## Number of contigs is 1373. Cumulated length is 33.8Mb.
## ST14TAS_WAI1878
## Number of contigs is 1499. Cumulated length is 33.85Mb.
## ST14TAS_WAI1879
## Number of contigs is 1199. Cumulated length is 33.46Mb.
## ST14TAS_WAI1880
## Number of contigs is 1356. Cumulated length is 33.51Mb.
## ST14TAS_WAI1881
## Number of contigs is 436. Cumulated length is 0.94Mb.
## ST14TAS_WAI1883
## Number of contigs is 311. Cumulated length is 0.71Mb.
## ST14TAS_WAI1892
## Number of contigs is 1599. Cumulated length is 34.03Mb.
## ST14TAS_WAI1895
## Number of contigs is 1341. Cumulated length is 33.79Mb.
## ST14TAS_WAI1901
## Number of contigs is 1448. Cumulated length is 33.82Mb.
## ST14TAS_WAI1903
## Number of contigs is 1566. Cumulated length is 33.3Mb.
## ST14TAS_WAI1904
## Number of contigs is 1391. Cumulated length is 33.22Mb.
## ST14TAS_WAI1919
## Number of contigs is 1123. Cumulated length is 34.07Mb.
## ST14TAS_WAI1922
## Number of contigs is 1745. Cumulated length is 33.02Mb.
## ST14TAS_WAI1939
## Number of contigs is 1235. Cumulated length is 33.2Mb.
## ST14TAS_WAI1941
## Number of contigs is 1049. Cumulated length is 33.51Mb.
## ST14TAS_WAI1955
## Number of contigs is 1099. Cumulated length is 33.4Mb.
## ST14TAS_WAI1957
## Number of contigs is 1074. Cumulated length is 32.42Mb.
## ST14TAS_WAI1965
## Number of contigs is 5091. Cumulated length is 32.64Mb.
## ST14TAS_WAI1966
## Number of contigs is 1230. Cumulated length is 32.98Mb.
## ST14TAS_WAI1967
## Number of contigs is 1209. Cumulated length is 32.46Mb.
## ST14TAS_WAI1968
## Number of contigs is 1567. Cumulated length is 33.53Mb.
## ST14TAS_WAI1969
## Number of contigs is 1108. Cumulated length is 32.73Mb.
## ST14TAS_WAI1970
## Number of contigs is 1114. Cumulated length is 32.73Mb.
## ST14TAS_WAI1970D
## Number of contigs is 1152. Cumulated length is 32.72Mb.
## ST14TAS_WAI1971
## Number of contigs is 2929. Cumulated length is 40.85Mb.
## ST14TAS_WAI1972
## Number of contigs is 1088. Cumulated length is 33.08Mb.
## ST14TAS_WAI1993
## Number of contigs is 966. Cumulated length is 34.51Mb.
## ST14TAS_WAI1998
## Number of contigs is 1767. Cumulated length is 38.45Mb.
## ST14TAS_WAI2000
## Number of contigs is 1109. Cumulated length is 33.86Mb.
## ST14TAS_WAI2029
## Number of contigs is 3744. Cumulated length is 33.23Mb.
## ST14TAS_WAI2031
## Number of contigs is 1028. Cumulated length is 33.43Mb.
## ST14TAS_WAI2045
## Number of contigs is 1183. Cumulated length is 33.49Mb.
## ST14TAS_WAI2047
## Number of contigs is 1252. Cumulated length is 33.9Mb.
## ST14TAS_WAI2059
## Number of contigs is 1422. Cumulated length is 33.27Mb.
## ST14TAS_WAI2060
## Number of contigs is 1107. Cumulated length is 33.9Mb.
## ST14TAS_WAI2061
## Number of contigs is 1025. Cumulated length is 33.34Mb.
## ST14TAS_WAI2073
## Number of contigs is 1075. Cumulated length is 33.6Mb.
## ST14TAS_WAI2077
## Number of contigs is 1876. Cumulated length is 33.88Mb.
## ST14TAS_WAI2203
## Number of contigs is 1029. Cumulated length is 33.3Mb.
## ST14TAS_WAI2204
## Number of contigs is 1092. Cumulated length is 33.64Mb.
## ST14TAS_WAI2206
## Number of contigs is 1107. Cumulated length is 33.4Mb.
## ST14TAS_WAI2208
## Number of contigs is 1032. Cumulated length is 34.01Mb.
## ST14TAS_WAI2210
## Number of contigs is 983. Cumulated length is 32.73Mb.
## ST14TAS_WAI2216
## Number of contigs is 1052. Cumulated length is 33.7Mb.
## ST14TAS_WAI2226
## Number of contigs is 1456. Cumulated length is 33.52Mb.
## ST14TAS_WAI2228
## Number of contigs is 1235. Cumulated length is 33.31Mb.
## ST14TAS_WAI2230
## Number of contigs is 1292. Cumulated length is 33.27Mb.
## ST14TAS_WAI2232
## Number of contigs is 1329. Cumulated length is 33.78Mb.
## ST14UK_Biog_TMW07D8
## Number of contigs is 1546. Cumulated length is 33.12Mb.
## ST15NZ_St_15601_1
## Number of contigs is 1042. Cumulated length is 33.28Mb.
## ST15NZ_St_15601_10
## Number of contigs is 1157. Cumulated length is 33.21Mb.
## ST15NZ_St_15601_11
## Number of contigs is 1124. Cumulated length is 33.3Mb.
## ST15NZ_St_15601_12
## Number of contigs is 1150. Cumulated length is 33.29Mb.
## ST15NZ_St_15601_13
## Number of contigs is 1090. Cumulated length is 33.32Mb.
## ST15NZ_St_15601_14
## Number of contigs is 1061. Cumulated length is 33.28Mb.
## ST15NZ_St_15601_15
## Number of contigs is 1054. Cumulated length is 33.19Mb.
## ST15NZ_St_15601_16
## Number of contigs is 1103. Cumulated length is 33.28Mb.
## ST15NZ_St_15601_17
## Number of contigs is 1057. Cumulated length is 33.27Mb.
## ST15NZ_St_15601_18
## Number of contigs is 1052. Cumulated length is 33.29Mb.
## ST15NZ_St_15601_19
## Number of contigs is 1132. Cumulated length is 33.23Mb.
## ST15NZ_St_15601_2
## Number of contigs is 1121. Cumulated length is 33.26Mb.
## ST15NZ_St_15601_20
## Number of contigs is 1233. Cumulated length is 33.83Mb.
## ST15NZ_St_15601_3
## Number of contigs is 1131. Cumulated length is 33.3Mb.
## ST15NZ_St_15601_4
## Number of contigs is 1160. Cumulated length is 33.32Mb.
## ST15NZ_St_15601_5
## Number of contigs is 1139. Cumulated length is 33.98Mb.
## ST15NZ_St_15601_6
## Number of contigs is 1054. Cumulated length is 33.3Mb.
## ST15NZ_St_15601_7
## Number of contigs is 1128. Cumulated length is 33.28Mb.
## ST15NZ_St_15601_8
## Number of contigs is 1118. Cumulated length is 33.21Mb.
## ST15NZ_St_15601_9
## Number of contigs is 1205. Cumulated length is 33.97Mb.
## ST15NZ_St_15640_1
## Number of contigs is 1173. Cumulated length is 33.51Mb.
## ST15NZ_St_15640_10
## Number of contigs is 1073. Cumulated length is 34.06Mb.
## ST15NZ_St_15640_11
## Number of contigs is 1052. Cumulated length is 33.44Mb.
## ST15NZ_St_15640_12
## Number of contigs is 1060. Cumulated length is 34.01Mb.
## ST15NZ_St_15640_2
## Number of contigs is 1032. Cumulated length is 34.05Mb.
## ST15NZ_St_15640_3
## Number of contigs is 1009. Cumulated length is 33.75Mb.
## ST15NZ_St_15640_4
## Number of contigs is 1091. Cumulated length is 33.73Mb.
## ST15NZ_St_15640_5
## Number of contigs is 1078. Cumulated length is 34.05Mb.
## ST15NZ_St_15640_6
## Number of contigs is 1084. Cumulated length is 34.07Mb.
## ST15NZ_St_15640_7
## Number of contigs is 2560. Cumulated length is 34.6Mb.
## ST15NZ_St_15640_8
## Number of contigs is 999. Cumulated length is 33.74Mb.
## ST15NZ_St_15640_9
## Number of contigs is 997. Cumulated length is 33.46Mb.
## ST15NZ_St_15642_1
## Number of contigs is 1131. Cumulated length is 33.4Mb.
## ST15NZ_St_15642_10
## Number of contigs is 990. Cumulated length is 32.78Mb.
## ST15NZ_St_15642_11
## Number of contigs is 969. Cumulated length is 32.6Mb.
## ST15NZ_St_15642_12
## Number of contigs is 949. Cumulated length is 33.14Mb.
## ST15NZ_St_15642_13
## Number of contigs is 1042. Cumulated length is 33.26Mb.
## ST15NZ_St_15642_14
## Number of contigs is 1067. Cumulated length is 37.11Mb.
## ST15NZ_St_15642_15
## Number of contigs is 1418. Cumulated length is 33.34Mb.
## ST15NZ_St_15642_16
## Number of contigs is 1020. Cumulated length is 32.86Mb.
## ST15NZ_St_15642_17
## Number of contigs is 1268. Cumulated length is 33.46Mb.
## ST15NZ_St_15642_18
## Number of contigs is 1239. Cumulated length is 33.55Mb.
## ST15NZ_St_15642_19
## Number of contigs is 1580. Cumulated length is 39.14Mb.
## ST15NZ_St_15642_2
## Number of contigs is 1225. Cumulated length is 34.08Mb.
## ST15NZ_St_15642_20
## Number of contigs is 1091. Cumulated length is 32.64Mb.
## ST15NZ_St_15642_21
## Number of contigs is 1151. Cumulated length is 33.3Mb.
## ST15NZ_St_15642_22
## Number of contigs is 1069. Cumulated length is 33.41Mb.
## ST15NZ_St_15642_23
## Number of contigs is 1115. Cumulated length is 33.44Mb.
## ST15NZ_St_15642_3
## Number of contigs is 1124. Cumulated length is 33.15Mb.
## ST15NZ_St_15642_4
## Number of contigs is 2291. Cumulated length is 34.54Mb.
## ST15NZ_St_15642_8
## Number of contigs is 1699. Cumulated length is 33.81Mb.
## ST15NZ_St_15642_9
## Number of contigs is 1126. Cumulated length is 33.71Mb.
## ST15ORE_Mad_A1
## Number of contigs is 1123. Cumulated length is 35.29Mb.
## ST15ORE_Mad_A2
## Number of contigs is 1096. Cumulated length is 34.81Mb.
## ST15ORE_Mad_A3
## Number of contigs is 1151. Cumulated length is 35.19Mb.
## ST15ORE_Mad_A4
## Number of contigs is 1117. Cumulated length is 35.35Mb.
## ST15ORE_Mad_A5
## Number of contigs is 1188. Cumulated length is 35.68Mb.
## ST15ORE_Mad_A6
## Number of contigs is 1097. Cumulated length is 35.06Mb.
## ST15ORE_Mad_A7
## Number of contigs is 1175. Cumulated length is 35.31Mb.
## ST15ORE_Mad_B1
## Number of contigs is 1139. Cumulated length is 35.03Mb.
## ST15ORE_Mad_B3
## Number of contigs is 1172. Cumulated length is 34.64Mb.
## ST15ORE_Mad_B4
## Number of contigs is 1049. Cumulated length is 34.27Mb.
## ST15ORE_Mad_B5
## Number of contigs is 1081. Cumulated length is 35.22Mb.
## ST15ORE_Mad_C1
## Number of contigs is 1102. Cumulated length is 35.22Mb.
## ST15ORE_Mad_C2
## Number of contigs is 1126. Cumulated length is 34.52Mb.
## ST15ORE_Mad_C3
## Number of contigs is 1266. Cumulated length is 35.52Mb.
## ST15ORE_Mad_C4
## Number of contigs is 999. Cumulated length is 34.33Mb.
## ST15ORE_Mad_C5
## Number of contigs is 1172. Cumulated length is 35.49Mb.
## ST15ORE_Mad_C6
## Number of contigs is 1196. Cumulated length is 34.74Mb.
## ST15ORE_Mad_C7
## Number of contigs is 1067. Cumulated length is 34.53Mb.
## ST15ORE_Mad_D1
## Number of contigs is 1197. Cumulated length is 35.28Mb.
## ST15ORE_Mad_D2
## Number of contigs is 1122. Cumulated length is 34.7Mb.
## ST15ORE_Mad_D3
## Number of contigs is 1146. Cumulated length is 35.36Mb.
## ST15ORE_Mad_D4
## Number of contigs is 1193. Cumulated length is 35.54Mb.
## ST15ORE_Mad_D5
## Number of contigs is 1178. Cumulated length is 34.84Mb.
## ST15ORE_Mad_D6
## Number of contigs is 1102. Cumulated length is 34.53Mb.
## ST15ORE_Mad_E1
## Number of contigs is 1116. Cumulated length is 35.03Mb.
## ST15ORE_Mad_E2
## Number of contigs is 1154. Cumulated length is 34.61Mb.
## ST15ORE_Mad_E3
## Number of contigs is 1140. Cumulated length is 34.59Mb.
## ST15ORE_Mad_E4
## Number of contigs is 1038. Cumulated length is 34.44Mb.
## ST15ORE_Mad_E5
## Number of contigs is 1089. Cumulated length is 35.33Mb.
## ST15ORE_Mad_E6
## Number of contigs is 1090. Cumulated length is 35.26Mb.
## ST15ORE_Mad_E7
## Number of contigs is 1208. Cumulated length is 36.0Mb.
## ST15ORE_Mad_F1
## Number of contigs is 1246. Cumulated length is 35.02Mb.
## ST15ORE_Mad_F2
## Number of contigs is 1089. Cumulated length is 34.17Mb.
## ST15ORE_Mad_F3
## Number of contigs is 1286. Cumulated length is 34.98Mb.
## ST15ORE_Mad_F4
## Number of contigs is 1140. Cumulated length is 34.93Mb.
## ST15ORE_Mad_F5
## Number of contigs is 1023. Cumulated length is 32.72Mb.
## ST15ORE_Mad_F6
## Number of contigs is 1105. Cumulated length is 35.23Mb.
## ST15ORE_Mad_G1
## Number of contigs is 1208. Cumulated length is 35.56Mb.
## ST15ORE_Mad_G2
## Number of contigs is 1324. Cumulated length is 35.13Mb.
## ST15ORE_Mad_G3
## Number of contigs is 1103. Cumulated length is 34.3Mb.
## ST15ORE_Mad_G4
## Number of contigs is 1146. Cumulated length is 34.38Mb.
## ST15ORE_Mad_G5
## Number of contigs is 1230. Cumulated length is 35.56Mb.
## ST15ORE_Mad_H1
## Number of contigs is 1221. Cumulated length is 35.62Mb.
## ST15ORE_Mad_H2
## Number of contigs is 1098. Cumulated length is 34.46Mb.
## ST15ORE_Mad_H3
## Number of contigs is 1264. Cumulated length is 35.16Mb.
## ST15ORE_Mad_H4
## Number of contigs is 1222. Cumulated length is 35.16Mb.
## ST15ORE_Mad_H7
## Number of contigs is 1246. Cumulated length is 35.57Mb.
## ST15ORE_Ste_A1
## Number of contigs is 1216. Cumulated length is 35.37Mb.
## ST15ORE_Ste_A10
## Number of contigs is 1199. Cumulated length is 34.04Mb.
## ST15ORE_Ste_A11
## Number of contigs is 1166. Cumulated length is 35.35Mb.
## ST15ORE_Ste_A12
## Number of contigs is 1159. Cumulated length is 34.68Mb.
## ST15ORE_Ste_A13
## Number of contigs is 1054. Cumulated length is 34.69Mb.
## ST15ORE_Ste_A14
## Number of contigs is 1207. Cumulated length is 34.93Mb.
## ST15ORE_Ste_A15
## Number of contigs is 1193. Cumulated length is 35.01Mb.
## ST15ORE_Ste_A16
## Number of contigs is 1100. Cumulated length is 34.7Mb.
## ST15ORE_Ste_A17
## Number of contigs is 1186. Cumulated length is 34.53Mb.
## ST15ORE_Ste_A18
## Number of contigs is 1172. Cumulated length is 34.93Mb.
## ST15ORE_Ste_A19
## Number of contigs is 1127. Cumulated length is 35.41Mb.
## ST15ORE_Ste_A2
## Number of contigs is 1058. Cumulated length is 35.08Mb.
## ST15ORE_Ste_A20
## Number of contigs is 1076. Cumulated length is 34.99Mb.
## ST15ORE_Ste_A21
## Number of contigs is 1255. Cumulated length is 35.07Mb.
## ST15ORE_Ste_A22
## Number of contigs is 1142. Cumulated length is 34.92Mb.
## ST15ORE_Ste_A23
## Number of contigs is 1152. Cumulated length is 35.38Mb.
## ST15ORE_Ste_A24
## Number of contigs is 1102. Cumulated length is 34.95Mb.
## ST15ORE_Ste_A25
## Number of contigs is 1145. Cumulated length is 35.3Mb.
## ST15ORE_Ste_A26
## Number of contigs is 1188. Cumulated length is 35.06Mb.
## ST15ORE_Ste_A27
## Number of contigs is 1183. Cumulated length is 35.52Mb.
## ST15ORE_Ste_A3
## Number of contigs is 1141. Cumulated length is 34.74Mb.
## ST15ORE_Ste_A4
## Number of contigs is 1150. Cumulated length is 35.14Mb.
## ST15ORE_Ste_A5
## Number of contigs is 1058. Cumulated length is 35.17Mb.
## ST15ORE_Ste_A6
## Number of contigs is 1179. Cumulated length is 35.03Mb.
## ST15ORE_Ste_A7
## Number of contigs is 1243. Cumulated length is 35.48Mb.
## ST15ORE_Ste_A8
## Number of contigs is 1189. Cumulated length is 34.49Mb.
## ST15ORE_Ste_A9
## Number of contigs is 1171. Cumulated length is 35.14Mb.
## ST15ORE_Ste_B1
## Number of contigs is 1214. Cumulated length is 35.06Mb.
## ST15ORE_Ste_B10
## Number of contigs is 1162. Cumulated length is 35.43Mb.
## ST15ORE_Ste_B11
## Number of contigs is 1189. Cumulated length is 34.69Mb.
## ST15ORE_Ste_B12
## Number of contigs is 1158. Cumulated length is 35.34Mb.
## ST15ORE_Ste_B14
## Number of contigs is 1108. Cumulated length is 35.12Mb.
## ST15ORE_Ste_B15
## Number of contigs is 1101. Cumulated length is 34.83Mb.
## ST15ORE_Ste_B16
## Number of contigs is 1157. Cumulated length is 34.48Mb.
## ST15ORE_Ste_B17
## Number of contigs is 1096. Cumulated length is 34.88Mb.
## ST15ORE_Ste_B18
## Number of contigs is 1181. Cumulated length is 35.1Mb.
## ST15ORE_Ste_B19
## Number of contigs is 1208. Cumulated length is 35.48Mb.
## ST15ORE_Ste_B2
## Number of contigs is 1277. Cumulated length is 35.03Mb.
## ST15ORE_Ste_B20
## Number of contigs is 1093. Cumulated length is 34.08Mb.
## ST15ORE_Ste_B21
## Number of contigs is 1189. Cumulated length is 35.04Mb.
## ST15ORE_Ste_B22
## Number of contigs is 1158. Cumulated length is 34.98Mb.
## ST15ORE_Ste_B23
## Number of contigs is 1110. Cumulated length is 35.16Mb.
## ST15ORE_Ste_B24
## Number of contigs is 1235. Cumulated length is 34.88Mb.
## ST15ORE_Ste_B3
## Number of contigs is 1224. Cumulated length is 35.51Mb.
## ST15ORE_Ste_B4
## Number of contigs is 1247. Cumulated length is 35.0Mb.
## ST15ORE_Ste_B5
## Number of contigs is 1081. Cumulated length is 35.04Mb.
## ST15ORE_Ste_B6
## Number of contigs is 1169. Cumulated length is 35.53Mb.
## ST15ORE_Ste_B7
## Number of contigs is 1132. Cumulated length is 34.94Mb.
## ST15ORE_Ste_B8
## Number of contigs is 1133. Cumulated length is 34.56Mb.
## ST15ORE_Ste_B9
## Number of contigs is 1227. Cumulated length is 35.61Mb.
## ST16ALG_Biog_Alg74
## Number of contigs is 936. Cumulated length is 33.38Mb.
## ST16CH_1A1
## Number of contigs is 1112. Cumulated length is 32.79Mb.
## ST16CH_1A11
## Number of contigs is 854. Cumulated length is 33.31Mb.
## ST16CH_1A27
## Number of contigs is 784. Cumulated length is 33.8Mb.
## ST16CH_1A57
## Number of contigs is 788. Cumulated length is 32.65Mb.
## ST16CH_1B31
## Number of contigs is 940. Cumulated length is 33.87Mb.
## ST16CH_1B73
## Number of contigs is 943. Cumulated length is 33.34Mb.
## ST16CH_1B8
## Number of contigs is 832. Cumulated length is 33.89Mb.
## ST16CH_1C12
## Number of contigs is 849. Cumulated length is 33.77Mb.
## ST16CH_1C31
## Number of contigs is 918. Cumulated length is 33.36Mb.
## ST16CH_1C52
## Number of contigs is 957. Cumulated length is 34.02Mb.
## ST16CH_1C65
## Number of contigs is 1112. Cumulated length is 32.69Mb.
## ST16CH_1D1
## Number of contigs is 941. Cumulated length is 32.99Mb.
## ST16CH_1D15
## Number of contigs is 1030. Cumulated length is 32.6Mb.
## ST16CH_1D15_2
## Number of contigs is 913. Cumulated length is 32.74Mb.
## ST16CH_1D23
## Number of contigs is 3413. Cumulated length is 34.38Mb.
## ST16CH_1D8
## Number of contigs is 901. Cumulated length is 32.83Mb.
## ST16CH_1D8_2
## Number of contigs is 1464. Cumulated length is 32.7Mb.
## ST16CH_1E21
## Number of contigs is 952. Cumulated length is 33.14Mb.
## ST16CH_1E43
## Number of contigs is 1058. Cumulated length is 33.4Mb.
## ST16CH_1E52
## Number of contigs is 1148. Cumulated length is 33.71Mb.
## ST16CH_1E52_2
## Number of contigs is 1151. Cumulated length is 33.6Mb.
## ST16CH_1E70
## Number of contigs is 1104. Cumulated length is 14.12Mb.
## ST16CH_1F1
## Number of contigs is 856. Cumulated length is 31.96Mb.
## ST16CH_1F11
## Number of contigs is 1617. Cumulated length is 33.44Mb.
## ST16CH_1F19
## Number of contigs is 786. Cumulated length is 32.56Mb.
## ST16CH_1F4
## Number of contigs is 1217. Cumulated length is 32.91Mb.
## ST16CH_1G30
## Number of contigs is 639. Cumulated length is 30.93Mb.
## ST16CH_1G47
## Number of contigs is 930. Cumulated length is 32.69Mb.
## ST16CH_1G8
## Number of contigs is 1007. Cumulated length is 32.8Mb.
## ST16CH_1H12
## Number of contigs is 802. Cumulated length is 30.98Mb.
## ST16CH_1H32
## Number of contigs is 898. Cumulated length is 33.72Mb.
## ST16CH_1H34
## Number of contigs is 1024. Cumulated length is 33.84Mb.
## ST16CH_1I10
## Number of contigs is 958. Cumulated length is 33.27Mb.
## ST16CH_1I19
## Number of contigs is 284. Cumulated length is 12.85Mb.
## ST16CH_1I3
## Number of contigs is 958. Cumulated length is 32.96Mb.
## ST16CH_1K16
## Number of contigs is 1217. Cumulated length is 33.11Mb.
## ST16CH_1K29
## Number of contigs is 1027. Cumulated length is 32.59Mb.
## ST16CH_1K37
## Number of contigs is 272. Cumulated length is 12.82Mb.
## ST16CH_1K42
## Number of contigs is 995. Cumulated length is 34.29Mb.
## ST16CH_1L32
## Number of contigs is 865. Cumulated length is 34.06Mb.
## ST16CH_1L40
## Number of contigs is 69. Cumulated length is 0.28Mb.
## ST16CH_1L42
## Number of contigs is 2265. Cumulated length is 13.85Mb.
## ST16CH_1L46
## Number of contigs is 1195. Cumulated length is 33.57Mb.
## ST16CH_1M21
## Number of contigs is 922. Cumulated length is 32.49Mb.
## ST16CH_1M28
## Number of contigs is 882. Cumulated length is 33.82Mb.
## ST16CH_1M33
## Number of contigs is 864. Cumulated length is 33.68Mb.
## ST16CH_1M59
## Number of contigs is 842. Cumulated length is 32.8Mb.
## ST16CH_1N1
## Number of contigs is 912. Cumulated length is 33.64Mb.
## ST16CH_1N25
## Number of contigs is 982. Cumulated length is 33.59Mb.
## ST16CH_1N6
## Number of contigs is 904. Cumulated length is 31.83Mb.
## ST16CH_1O25
## Number of contigs is 877. Cumulated length is 34.05Mb.
## ST16CH_1O3
## Number of contigs is 768. Cumulated length is 32.87Mb.
## ST16CH_1O40
## Number of contigs is 960. Cumulated length is 32.84Mb.
## ST16CH_1O65
## Number of contigs is 783. Cumulated length is 32.05Mb.
## ST16CH_1P22
## Number of contigs is 1058. Cumulated length is 33.12Mb.
## ST16CH_1P35
## Number of contigs is 869. Cumulated length is 33.15Mb.
## ST16CH_1P56
## Number of contigs is 14. Cumulated length is 0.03Mb.
## ST16CH_1P56_2
## Number of contigs is 932. Cumulated length is 33.14Mb.
## ST16CH_1P7
## Number of contigs is 0. Cumulated length is 0.0Mb.
## Traceback (most recent call last):
## File "/home/alice/Common_scripts/Stats_from_fasta.py", line 78, in <module>
## out.write(f"Smallest contig length\t{length_list[-1]}\n")
## IndexError: list index out of range
## ST16CH_1P7_2
## Number of contigs is 926. Cumulated length is 32.73Mb.
## ST16CH_1Q10
## Number of contigs is 836. Cumulated length is 32.66Mb.
## ST16CH_1Q24
## Number of contigs is 1032. Cumulated length is 32.21Mb.
## ST16CH_1Q48
## Number of contigs is 1107. Cumulated length is 33.97Mb.
## ST16CH_1R15
## Number of contigs is 13. Cumulated length is 0.02Mb.
## ST16CH_1R15_2
## Number of contigs is 6480. Cumulated length is 28.62Mb.
## ST16CH_1R24
## Number of contigs is 873. Cumulated length is 33.41Mb.
## ST16CH_1R36
## Number of contigs is 1018. Cumulated length is 33.35Mb.
## ST16CH_1R5
## Number of contigs is 894. Cumulated length is 33.58Mb.
## ST16CH_1S10
## Number of contigs is 762. Cumulated length is 33.16Mb.
## ST16CH_1S33
## Number of contigs is 810. Cumulated length is 33.1Mb.
## ST16CH_1S7
## Number of contigs is 970. Cumulated length is 32.98Mb.
## ST16CH_1S9
## Number of contigs is 816. Cumulated length is 32.78Mb.
## ST16CH_1T2
## Number of contigs is 1070. Cumulated length is 33.67Mb.
## ST16CH_1T25
## Number of contigs is 978. Cumulated length is 32.98Mb.
## ST16CH_1T52
## Number of contigs is 994. Cumulated length is 32.87Mb.
## ST16CH_1U1
## Number of contigs is 953. Cumulated length is 33.45Mb.
## ST16CH_1U30
## Number of contigs is 1030. Cumulated length is 33.79Mb.
## ST16CH_1U6
## Number of contigs is 834. Cumulated length is 32.77Mb.
## ST16CH_1U9
## Number of contigs is 1095. Cumulated length is 33.09Mb.
## ST16CH_1V12
## Number of contigs is 1237. Cumulated length is 32.08Mb.
## ST16CH_1V20
## Number of contigs is 924. Cumulated length is 33.23Mb.
## ST16CH_1V4
## Number of contigs is 1151. Cumulated length is 32.84Mb.
## ST16CH_1V50
## Number of contigs is 1256. Cumulated length is 33.6Mb.
## ST16CH_1W18
## Number of contigs is 974. Cumulated length is 33.18Mb.
## ST16CH_1W32
## Number of contigs is 1311. Cumulated length is 33.67Mb.
## ST16CH_1W9
## Number of contigs is 1015. Cumulated length is 33.94Mb.
## ST16CH_1X1
## Number of contigs is 859. Cumulated length is 32.78Mb.
## ST16CH_1X14
## Number of contigs is 990. Cumulated length is 32.79Mb.
## ST16CH_1X23
## Number of contigs is 883. Cumulated length is 33.33Mb.
## ST16CH_1X7
## Number of contigs is 889. Cumulated length is 32.83Mb.
## ST16CH_2C1
## Number of contigs is 897. Cumulated length is 32.73Mb.
## ST16CH_2C2
## Number of contigs is 883. Cumulated length is 33.05Mb.
## ST16CH_2C5
## Number of contigs is 1032. Cumulated length is 33.29Mb.
## ST16CH_2C7
## Number of contigs is 886. Cumulated length is 33.41Mb.
## ST16CH_2G10
## Number of contigs is 944. Cumulated length is 31.55Mb.
## ST16CH_2G18
## Number of contigs is 827. Cumulated length is 33.06Mb.
## ST16CH_2G34
## Number of contigs is 961. Cumulated length is 33.45Mb.
## ST16CH_2G4
## Number of contigs is 947. Cumulated length is 32.41Mb.
## ST16CH_2N5
## Number of contigs is 865. Cumulated length is 33.22Mb.
## ST16CH_2O1
## Number of contigs is 1283. Cumulated length is 32.91Mb.
## ST16CH_2O4
## Number of contigs is 1120. Cumulated length is 33.55Mb.
## ST16CH_2O5
## Number of contigs is 2930. Cumulated length is 32.56Mb.
## ST16CH_2P1
## Number of contigs is 1390. Cumulated length is 33.48Mb.
## ST16CH_2P3
## Number of contigs is 878. Cumulated length is 33.24Mb.
## ST16CH_2P5
## Number of contigs is 961. Cumulated length is 33.02Mb.
## ST16CH_2P7
## Number of contigs is 915. Cumulated length is 33.24Mb.
## ST16CH_2U14
## Number of contigs is 0. Cumulated length is 0.0Mb.
## Traceback (most recent call last):
## File "/home/alice/Common_scripts/Stats_from_fasta.py", line 78, in <module>
## out.write(f"Smallest contig length\t{length_list[-1]}\n")
## IndexError: list index out of range
## ST16CH_2U14_2
## Number of contigs is 948. Cumulated length is 33.72Mb.
## ST16CH_2U2
## Number of contigs is 1198. Cumulated length is 33.0Mb.
## ST16CH_2U24
## Number of contigs is 886. Cumulated length is 33.62Mb.
## ST16CH_2U7
## Number of contigs is 857. Cumulated length is 32.88Mb.
## ST16CH_2X10
## Number of contigs is 6022. Cumulated length is 16.3Mb.
## ST16CH_2X1xx
## Number of contigs is 839. Cumulated length is 34.02Mb.
## ST16CH_2X2
## Number of contigs is 829. Cumulated length is 33.69Mb.
## ST16CH_2Z1
## Number of contigs is 1167. Cumulated length is 32.48Mb.
## ST16CH_2gamma1
## Number of contigs is 1053. Cumulated length is 32.75Mb.
## ST16CH_3A16
## Number of contigs is 841. Cumulated length is 33.03Mb.
## ST16CH_3A31
## Number of contigs is 868. Cumulated length is 33.06Mb.
## ST16CH_3A36
## Number of contigs is 1117. Cumulated length is 33.05Mb.
## ST16CH_3A51
## Number of contigs is 830. Cumulated length is 33.09Mb.
## ST16CH_3B1
## Number of contigs is 983. Cumulated length is 33.54Mb.
## ST16CH_3B19
## Number of contigs is 164. Cumulated length is 28.5Mb.
## ST16CH_3B36
## Number of contigs is 847. Cumulated length is 33.11Mb.
## ST16CH_3B8
## Number of contigs is 940. Cumulated length is 33.22Mb.
## ST16CH_3C19
## Number of contigs is 1029. Cumulated length is 33.43Mb.
## ST16CH_3C23
## Number of contigs is 951. Cumulated length is 32.3Mb.
## ST16CH_3C6
## Number of contigs is 944. Cumulated length is 32.6Mb.
## ST16CH_3C81
## Number of contigs is 961. Cumulated length is 31.96Mb.
## ST16CH_3D1
## Number of contigs is 1030. Cumulated length is 33.78Mb.
## ST16CH_3D10
## Number of contigs is 895. Cumulated length is 33.67Mb.
## ST16CH_3D6
## Number of contigs is 1214. Cumulated length is 33.23Mb.
## ST16CH_3D7
## Number of contigs is 840. Cumulated length is 33.04Mb.
## ST16CH_3E23
## Number of contigs is 880. Cumulated length is 33.38Mb.
## ST16CH_3E34
## Number of contigs is 1158. Cumulated length is 33.38Mb.
## ST16CH_3E45
## Number of contigs is 757. Cumulated length is 33.75Mb.
## ST16CH_3E9
## Number of contigs is 875. Cumulated length is 33.72Mb.
## ST16CH_3F2
## Number of contigs is 1010. Cumulated length is 34.21Mb.
## ST16CH_3F4
## Number of contigs is 783. Cumulated length is 33.31Mb.
## ST16CH_3F7
## Number of contigs is 879. Cumulated length is 33.63Mb.
## ST16CH_3F9
## Number of contigs is 839. Cumulated length is 33.23Mb.
## ST16CH_3G26
## Number of contigs is 797. Cumulated length is 32.52Mb.
## ST16CH_3G34
## Number of contigs is 5385. Cumulated length is 29.94Mb.
## ST16CH_3G46
## Number of contigs is 876. Cumulated length is 33.29Mb.
## ST16CH_3G6
## Number of contigs is 823. Cumulated length is 32.89Mb.
## ST16CH_3H26
## Number of contigs is 813. Cumulated length is 32.3Mb.
## ST16CH_3H33
## Number of contigs is 716. Cumulated length is 31.23Mb.
## ST16CH_3H33_2
## Number of contigs is 8949. Cumulated length is 29.83Mb.
## ST16CH_3H43
## Number of contigs is 7176. Cumulated length is 30.5Mb.
## ST16CH_3H49
## Number of contigs is 943. Cumulated length is 32.98Mb.
## ST16CH_3I14
## Number of contigs is 913. Cumulated length is 31.19Mb.
## ST16CH_3I23
## Number of contigs is 1091. Cumulated length is 33.16Mb.
## ST16CH_3I23_2
## Number of contigs is 954. Cumulated length is 33.39Mb.
## ST16CH_3I5
## Number of contigs is 1012. Cumulated length is 32.22Mb.
## ST16CH_3I5_2
## Number of contigs is 0. Cumulated length is 0.0Mb.
## Traceback (most recent call last):
## File "/home/alice/Common_scripts/Stats_from_fasta.py", line 78, in <module>
## out.write(f"Smallest contig length\t{length_list[-1]}\n")
## IndexError: list index out of range
## ST16CH_3K1
## Number of contigs is 814. Cumulated length is 32.5Mb.
## ST16CH_3K32
## Number of contigs is 991. Cumulated length is 33.77Mb.
## ST16CH_3K8
## Number of contigs is 1994. Cumulated length is 35.64Mb.
## ST16CH_3L2
## Number of contigs is 1369. Cumulated length is 33.13Mb.
## ST16CH_3L27
## Number of contigs is 2436. Cumulated length is 33.11Mb.
## ST16CH_3M19
## Number of contigs is 823. Cumulated length is 32.71Mb.
## ST16CH_3M24
## Number of contigs is 994. Cumulated length is 32.79Mb.
## ST16CH_3M3
## Number of contigs is 913. Cumulated length is 34.11Mb.
## ST16CH_3M36
## Number of contigs is 937. Cumulated length is 33.49Mb.
## ST16CH_3N27
## Number of contigs is 853. Cumulated length is 33.47Mb.
## ST16CH_3N35
## Number of contigs is 1043. Cumulated length is 33.45Mb.
## ST16CH_3N48
## Number of contigs is 814. Cumulated length is 32.48Mb.
## ST16CH_3N8
## Number of contigs is 908. Cumulated length is 33.32Mb.
## ST16CH_3O21
## Number of contigs is 902. Cumulated length is 34.22Mb.
## ST16CH_3O24
## Number of contigs is 763. Cumulated length is 32.79Mb.
## ST16CH_3O9
## Number of contigs is 850. Cumulated length is 32.94Mb.
## ST16CH_3P15
## Number of contigs is 934. Cumulated length is 33.9Mb.
## ST16CH_3P2
## Number of contigs is 961. Cumulated length is 32.87Mb.
## ST16CH_3P39
## Number of contigs is 839. Cumulated length is 33.6Mb.
## ST16CH_3Q24
## Number of contigs is 938. Cumulated length is 33.35Mb.
## ST16CH_3Q36
## Number of contigs is 839. Cumulated length is 33.9Mb.
## ST16CH_3Q9
## Number of contigs is 894. Cumulated length is 33.2Mb.
## ST16CH_3R1
## Number of contigs is 942. Cumulated length is 33.86Mb.
## ST16CH_3R26
## Number of contigs is 952. Cumulated length is 33.85Mb.
## ST16CH_3R32
## Number of contigs is 912. Cumulated length is 33.99Mb.
## ST16CH_3R39
## Number of contigs is 904. Cumulated length is 34.01Mb.
## ST16CH_3S1
## Number of contigs is 1059. Cumulated length is 33.73Mb.
## ST16CH_3S9
## Number of contigs is 893. Cumulated length is 32.67Mb.
## ST16CH_3T31
## Number of contigs is 871. Cumulated length is 33.38Mb.
## ST16CH_3T39
## Number of contigs is 906. Cumulated length is 32.89Mb.
## ST16CH_3T5
## Number of contigs is 926. Cumulated length is 33.34Mb.
## ST16CH_3U31
## Number of contigs is 33. Cumulated length is 2.53Mb.
## ST16CH_3U42
## Number of contigs is 814. Cumulated length is 33.0Mb.
## ST16CH_3U55
## Number of contigs is 827. Cumulated length is 32.2Mb.
## ST16CH_3V10
## Number of contigs is 1177. Cumulated length is 33.18Mb.
## ST16CH_3V27
## Number of contigs is 860. Cumulated length is 33.48Mb.
## ST16CH_3V30
## Number of contigs is 952. Cumulated length is 33.37Mb.
## ST16CH_3V43
## Number of contigs is 1008. Cumulated length is 32.81Mb.
## ST16CH_3W21
## Number of contigs is 927. Cumulated length is 33.9Mb.
## ST16CH_3W3
## Number of contigs is 957. Cumulated length is 33.77Mb.
## ST16CH_3W9
## Number of contigs is 1039. Cumulated length is 33.45Mb.
## ST16DK_Biog_DK1
## Number of contigs is 1167. Cumulated length is 32.65Mb.
## ST16DK_Biog_DK15
## Number of contigs is 1103. Cumulated length is 33.15Mb.
## ST16DK_Biog_DK32
## Number of contigs is 949. Cumulated length is 34.22Mb.
## ST16FR_Biog_FR1
## Number of contigs is 0. Cumulated length is 0.0Mb.
## Traceback (most recent call last):
## File "/home/alice/Common_scripts/Stats_from_fasta.py", line 78, in <module>
## out.write(f"Smallest contig length\t{length_list[-1]}\n")
## IndexError: list index out of range
## ST16FR_Biog_FR31
## Number of contigs is 1278. Cumulated length is 33.04Mb.
## ST16FR_Biog_FR5
## Number of contigs is 768. Cumulated length is 31.84Mb.
## ST16IRE_Biog_IR1
## Number of contigs is 977. Cumulated length is 33.21Mb.
## ST16IRE_Biog_IR16
## Number of contigs is 974. Cumulated length is 32.66Mb.
## ST16IRE_Biog_IR32
## Number of contigs is 944. Cumulated length is 33.74Mb.
## ST16KA_Biog_K1
## Number of contigs is 2209. Cumulated length is 32.8Mb.
## ST16KA_Biog_K32
## Number of contigs is 864. Cumulated length is 33.75Mb.
## ST16LE_Biog_L1
## Number of contigs is 968. Cumulated length is 34.37Mb.
## ST16LE_Biog_L15
## Number of contigs is 1182. Cumulated length is 33.77Mb.
## ST16LE_Biog_L37
## Number of contigs is 943. Cumulated length is 33.15Mb.
## ST16RU_Biog_R1
## Number of contigs is 878. Cumulated length is 33.5Mb.
## ST16RU_Biog_R19
## Number of contigs is 886. Cumulated length is 33.86Mb.
## ST16RU_Biog_R9
## Number of contigs is 1030. Cumulated length is 33.21Mb.
## ST16TN_Biog_TMW21F9
## Number of contigs is 2279. Cumulated length is 33.11Mb.
## ST16TN_Biog_TMW21H5
## Number of contigs is 1132. Cumulated length is 32.69Mb.
## ST17ISR_Biog_ISR35
## Number of contigs is 1329. Cumulated length is 33.3Mb.
## ST89CA_14CC22A
## Number of contigs is 978. Cumulated length is 33.15Mb.
## ST89CA_24CC32B
## Number of contigs is 950. Cumulated length is 33.22Mb.
## ST89CA_32CD21A
## Number of contigs is 1227. Cumulated length is 32.74Mb.
## ST90ORE_a12_3B_10
## Number of contigs is 1105. Cumulated length is 32.21Mb.
## ST90ORE_a12_3B_11
## Number of contigs is 1233. Cumulated length is 32.48Mb.
## ST90ORE_a12_3B_12
## Number of contigs is 1114. Cumulated length is 32.26Mb.
## ST90ORE_a12_3B_13
## Number of contigs is 41. Cumulated length is 0.07Mb.
## ST90ORE_a12_3B_14
## Number of contigs is 1196. Cumulated length is 33.12Mb.
## ST90ORE_a12_3B_15
## Number of contigs is 1116. Cumulated length is 32.45Mb.
## ST90ORE_a12_3B_17
## Number of contigs is 1092. Cumulated length is 31.88Mb.
## ST90ORE_a12_3B_18
## Number of contigs is 1179. Cumulated length is 33.0Mb.
## ST90ORE_a12_3B_19
## Number of contigs is 1250. Cumulated length is 32.3Mb.
## ST90ORE_a12_3B_2
## Number of contigs is 1193. Cumulated length is 32.61Mb.
## ST90ORE_a12_3B_20
## Number of contigs is 1112. Cumulated length is 32.31Mb.
## ST90ORE_a12_3B_21
## Number of contigs is 1144. Cumulated length is 32.23Mb.
## ST90ORE_a12_3B_3
## Number of contigs is 1144. Cumulated length is 32.83Mb.
## ST90ORE_a12_3B_4
## Number of contigs is 1097. Cumulated length is 32.37Mb.
## ST90ORE_a12_3B_5
## Number of contigs is 1115. Cumulated length is 32.54Mb.
## ST90ORE_a12_3B_6
## Number of contigs is 1162. Cumulated length is 31.99Mb.
## ST90ORE_a12_3B_7
## Number of contigs is 1207. Cumulated length is 32.66Mb.
## ST90ORE_a12_3B_8
## Number of contigs is 1197. Cumulated length is 32.34Mb.
## ST90ORE_a12_3B_9
## Number of contigs is 1098. Cumulated length is 32.43Mb.
## ST90ORE_a12_4A_1
## Number of contigs is 1244. Cumulated length is 32.92Mb.
## ST90ORE_a12_4A_10
## Number of contigs is 1126. Cumulated length is 32.31Mb.
## ST90ORE_a12_4A_11
## Number of contigs is 1260. Cumulated length is 32.98Mb.
## ST90ORE_a12_4A_2
## Number of contigs is 1111. Cumulated length is 32.03Mb.
## ST90ORE_a12_4A_4
## Number of contigs is 1173. Cumulated length is 32.78Mb.
## ST90ORE_a12_4A_5
## Number of contigs is 1145. Cumulated length is 32.31Mb.
## ST90ORE_a12_4A_6
## Number of contigs is 1153. Cumulated length is 32.44Mb.
## ST90ORE_a12_4A_7
## Number of contigs is 1246. Cumulated length is 32.49Mb.
## ST90ORE_a15_2A_11
## Number of contigs is 1194. Cumulated length is 31.83Mb.
## ST90ORE_a15_2A_13
## Number of contigs is 1212. Cumulated length is 33.26Mb.
## ST90ORE_a15_2A_14
## Number of contigs is 1060. Cumulated length is 31.44Mb.
## ST90ORE_a15_2A_15
## Number of contigs is 1234. Cumulated length is 32.23Mb.
## ST90ORE_a15_2A_16
## Number of contigs is 1125. Cumulated length is 32.2Mb.
## ST90ORE_a15_2A_20
## Number of contigs is 1273. Cumulated length is 32.74Mb.
## ST90ORE_a15_2A_6
## Number of contigs is 1203. Cumulated length is 33.2Mb.
## ST90ORE_a15_2A_7
## Number of contigs is 1109. Cumulated length is 32.34Mb.
## ST90ORE_a15_2A_8
## Number of contigs is 1104. Cumulated length is 32.56Mb.
## ST90ORE_a15_3B_1
## Number of contigs is 1157. Cumulated length is 32.36Mb.
## ST90ORE_a15_3B_10
## Number of contigs is 1207. Cumulated length is 32.56Mb.
## ST90ORE_a15_3B_13
## Number of contigs is 1218. Cumulated length is 32.4Mb.
## ST90ORE_a15_3B_15
## Number of contigs is 1200. Cumulated length is 31.86Mb.
## ST90ORE_a15_3B_18
## Number of contigs is 1259. Cumulated length is 32.04Mb.
## ST90ORE_a15_3B_19
## Number of contigs is 1307. Cumulated length is 33.22Mb.
## ST90ORE_a15_3B_3
## Number of contigs is 1230. Cumulated length is 33.06Mb.
## ST90ORE_a15_3B_4
## Number of contigs is 1120. Cumulated length is 32.51Mb.
## ST90ORE_a15_3B_5
## Number of contigs is 1241. Cumulated length is 33.05Mb.
## ST90ORE_a15_3B_6
## Number of contigs is 1122. Cumulated length is 32.33Mb.
## ST90ORE_a15_3B_9
## Number of contigs is 1154. Cumulated length is 32.75Mb.
## ST90ORE_a15_4A_10
## Number of contigs is 1107. Cumulated length is 32.41Mb.
## ST90ORE_a15_4A_11
## Number of contigs is 1169. Cumulated length is 32.62Mb.
## ST90ORE_a15_4A_13
## Number of contigs is 1227. Cumulated length is 32.75Mb.
## ST90ORE_a15_4A_15
## Number of contigs is 1224. Cumulated length is 32.37Mb.
## ST90ORE_a15_4A_17
## Number of contigs is 1293. Cumulated length is 32.94Mb.
## ST90ORE_a15_4A_19
## Number of contigs is 1218. Cumulated length is 32.69Mb.
## ST90ORE_a15_4A_2
## Number of contigs is 1199. Cumulated length is 32.14Mb.
## ST90ORE_a15_4A_3
## Number of contigs is 1130. Cumulated length is 31.42Mb.
## ST90ORE_a15_4A_4
## Number of contigs is 1116. Cumulated length is 31.63Mb.
## ST90ORE_a15_4A_7
## Number of contigs is 1217. Cumulated length is 32.77Mb.
## ST92ISR_Ar_11g
## Number of contigs is 1061. Cumulated length is 33.12Mb.
## ST92ISR_Ar_11i
## Number of contigs is 1014. Cumulated length is 32.6Mb.
## ST92ISR_Ar_12d
## Number of contigs is 1044. Cumulated length is 32.83Mb.
## ST92ISR_Ar_12e
## Number of contigs is 1071. Cumulated length is 33.28Mb.
## ST92ISR_Ar_12f
## Number of contigs is 1009. Cumulated length is 32.76Mb.
## ST92ISR_Ar_15a
## Number of contigs is 1067. Cumulated length is 32.65Mb.
## ST92ISR_Ar_15c
## Number of contigs is 1020. Cumulated length is 32.32Mb.
## ST92ISR_Ar_16a
## Number of contigs is 1158. Cumulated length is 33.11Mb.
## ST92ISR_Ar_16h
## Number of contigs is 973. Cumulated length is 31.3Mb.
## ST92ISR_Ar_17b
## Number of contigs is 1058. Cumulated length is 32.41Mb.
## ST92ISR_Ar_17d
## Number of contigs is 991. Cumulated length is 32.59Mb.
## ST92ISR_Ar_17e
## Number of contigs is 1124. Cumulated length is 32.8Mb.
## ST92ISR_Ar_17i
## Number of contigs is 1035. Cumulated length is 32.7Mb.
## ST92ISR_Ar_17r
## Number of contigs is 992. Cumulated length is 32.23Mb.
## ST92ISR_Ar_18b
## Number of contigs is 943. Cumulated length is 32.41Mb.
## ST92ISR_Ar_19e
## Number of contigs is 1098. Cumulated length is 33.29Mb.
## ST92ISR_Ar_1b
## Number of contigs is 958. Cumulated length is 32.02Mb.
## ST92ISR_Ar_1c
## Number of contigs is 972. Cumulated length is 31.96Mb.
## ST92ISR_Ar_1j
## Number of contigs is 1115. Cumulated length is 33.18Mb.
## ST92ISR_Ar_21a
## Number of contigs is 1014. Cumulated length is 32.25Mb.
## ST92ISR_Ar_22f
## Number of contigs is 992. Cumulated length is 33.28Mb.
## ST92ISR_Ar_2b
## Number of contigs is 987. Cumulated length is 32.86Mb.
## ST92ISR_Ar_2c
## Number of contigs is 976. Cumulated length is 31.71Mb.
## ST92ISR_Ar_2f
## Number of contigs is 1083. Cumulated length is 33.19Mb.
## ST92ISR_Ar_4b
## Number of contigs is 1046. Cumulated length is 33.0Mb.
## ST92ISR_Ar_4e
## Number of contigs is 953. Cumulated length is 31.22Mb.
## ST92ISR_Ar_4f
## Number of contigs is 1053. Cumulated length is 32.6Mb.
## ST92ISR_Ar_4g
## Number of contigs is 929. Cumulated length is 31.91Mb.
## ST92ISR_Ar_5a
## Number of contigs is 833. Cumulated length is 32.29Mb.
## ST92ISR_Ar_5g
## Number of contigs is 1030. Cumulated length is 32.88Mb.
## ST92TK_2an
## Number of contigs is 1224. Cumulated length is 32.18Mb.
## ST92UK_A4
## Number of contigs is 957. Cumulated length is 33.78Mb.
## ST92UK_Pla2
## Number of contigs is 868. Cumulated length is 33.49Mb.
## ST92UK_XB16_1
## Number of contigs is 940. Cumulated length is 31.81Mb.
## ST92YE_1
## Number of contigs is 3067. Cumulated length is 32.73Mb.
## ST92YE_4
## Number of contigs is 961. Cumulated length is 32.78Mb.
## ST93IND_11a2
## Number of contigs is 1081. Cumulated length is 33.08Mb.
## ST93IND_28a1
## Number of contigs is 897. Cumulated length is 32.98Mb.
## ST93URU_EE3b_1
## Number of contigs is 948. Cumulated length is 32.74Mb.
## ST93URU_EE4a_1
## Number of contigs is 920. Cumulated length is 32.86Mb.
## ST93URU_LC16_2
## Number of contigs is 1030. Cumulated length is 32.51Mb.
## ST94CNR_C3b1
## Number of contigs is 1000. Cumulated length is 33.0Mb.
## ST94KE_MF1a
## Number of contigs is 760. Cumulated length is 32.84Mb.
## ST94KE_MI1a
## Number of contigs is 759. Cumulated length is 33.08Mb.
## ST95CH_3B2a
## Number of contigs is 882. Cumulated length is 33.0Mb.
## ST95CH_5A1a
## Number of contigs is 792. Cumulated length is 30.55Mb.
## ST95UR_EC2_2
## Number of contigs is 944. Cumulated length is 32.88Mb.
## ST99CH_28
## Number of contigs is 916. Cumulated length is 33.44Mb.
## ST99CH_3A1
## Number of contigs is 1030. Cumulated length is 33.27Mb.
## ST99CH_3A10
## Number of contigs is 955. Cumulated length is 32.38Mb.
## ST99CH_3A2
## Number of contigs is 1027. Cumulated length is 33.66Mb.
## ST99CH_3A4
## Number of contigs is 1058. Cumulated length is 33.3Mb.
## ST99CH_3A5
## Number of contigs is 928. Cumulated length is 32.75Mb.
## ST99CH_3A6
## Number of contigs is 906. Cumulated length is 32.41Mb.
## ST99CH_3A8
## Number of contigs is 972. Cumulated length is 33.72Mb.
## ST99CH_3A9
## Number of contigs is 943. Cumulated length is 33.18Mb.
## ST99CH_3B2
## Number of contigs is 1008. Cumulated length is 32.92Mb.
## ST99CH_3B4
## Number of contigs is 1020. Cumulated length is 33.25Mb.
## ST99CH_3B8
## Number of contigs is 970. Cumulated length is 33.41Mb.
## ST99CH_3C4
## Number of contigs is 1084. Cumulated length is 34.17Mb.
## ST99CH_3C7
## Number of contigs is 1016. Cumulated length is 32.93Mb.
## ST99CH_3D1
## Number of contigs is 1009. Cumulated length is 34.1Mb.
## ST99CH_3D3
## Number of contigs is 1102. Cumulated length is 33.98Mb.
## ST99CH_3D5
## Number of contigs is 974. Cumulated length is 33.39Mb.
## ST99CH_3D7
## Number of contigs is 865. Cumulated length is 32.57Mb.
## ST99CH_3D8
## Number of contigs is 981. Cumulated length is 33.52Mb.
## ST99CH_3F1
## Number of contigs is 996. Cumulated length is 32.59Mb.
## ST99CH_3F2
## Number of contigs is 1006. Cumulated length is 33.39Mb.
## ST99CH_3F3
## Number of contigs is 895. Cumulated length is 32.05Mb.
## ST99CH_3F4
## Number of contigs is 877. Cumulated length is 32.99Mb.
## ST99CH_3F5
## Number of contigs is 1057. Cumulated length is 34.14Mb.
## ST99CH_3G2
## Number of contigs is 1096. Cumulated length is 33.54Mb.
## ST99CH_3G3
## Number of contigs is 891. Cumulated length is 32.77Mb.
## ST99CH_3G6
## Number of contigs is 961. Cumulated length is 33.15Mb.
## ST99CH_3H1
## Number of contigs is 905. Cumulated length is 32.77Mb.
## ST99CH_3H3
## Number of contigs is 935. Cumulated length is 32.59Mb.
## ST99CH_3H4
## Number of contigs is 1033. Cumulated length is 33.78Mb.
## ST99CH_SW39
## Number of contigs is 1011. Cumulated length is 33.91Mb.
## ST99CH_SW5
## Number of contigs is 971. Cumulated length is 34.04Mb.
## STnnJGI_SRR4235061
## Number of contigs is 981. Cumulated length is 33.25Mb.
## STnnJGI_SRR4235062
## Number of contigs is 1068. Cumulated length is 35.24Mb.
## STnnJGI_SRR4235063
## Number of contigs is 1248. Cumulated length is 35.18Mb.
## STnnJGI_SRR4235064
## Number of contigs is 1120. Cumulated length is 35.1Mb.
## STnnJGI_SRR4235065
## Number of contigs is 1063. Cumulated length is 35.13Mb.
## STnnJGI_SRR4235066
## Number of contigs is 955. Cumulated length is 35.38Mb.
## STnnJGI_SRR4235067
## Number of contigs is 1060. Cumulated length is 35.78Mb.
## STnnJGI_SRR4235068
## Number of contigs is 1200. Cumulated length is 35.75Mb.
## STnnJGI_SRR4235069
## Number of contigs is 967. Cumulated length is 36.2Mb.
## STnnJGI_SRR4235070
## Number of contigs is 998. Cumulated length is 36.05Mb.
## STnnJGI_SRR4235071
## Number of contigs is 855. Cumulated length is 34.68Mb.
## STnnJGI_SRR4235072
## Number of contigs is 978. Cumulated length is 36.2Mb.
## STnnJGI_SRR4235073
## Number of contigs is 1073. Cumulated length is 34.64Mb.
## STnnJGI_SRR4235074
## Number of contigs is 989. Cumulated length is 35.42Mb.
## STnnJGI_SRR4235075
## Number of contigs is 849. Cumulated length is 34.48Mb.
## STnnJGI_SRR4235076
## Number of contigs is 1160. Cumulated length is 36.21Mb.
## STnnJGI_SRR4235077
## Number of contigs is 995. Cumulated length is 35.31Mb.
## STnnJGI_SRR4235078
## Number of contigs is 900. Cumulated length is 35.78Mb.
## STnnJGI_SRR4235079
## Number of contigs is 1018. Cumulated length is 35.67Mb.
## STnnJGI_SRR4235080
## Number of contigs is 983. Cumulated length is 33.18Mb.
## STnnJGI_SRR4235081
## Number of contigs is 1023. Cumulated length is 34.38Mb.
## STnnJGI_SRR4235082
## Number of contigs is 910. Cumulated length is 34.18Mb.
## STnnJGI_SRR4235083
## Number of contigs is 1090. Cumulated length is 35.48Mb.
## STnnJGI_SRR4235084
## Number of contigs is 1045. Cumulated length is 35.89Mb.
## STnnJGI_SRR4235085
## Number of contigs is 1031. Cumulated length is 36.01Mb.
## STnnJGI_SRR4235086
## Number of contigs is 985. Cumulated length is 35.2Mb.
## STnnJGI_SRR4235087
## Number of contigs is 1011. Cumulated length is 35.38Mb.
## STnnJGI_SRR4235088
## Number of contigs is 893. Cumulated length is 35.46Mb.
## STnnJGI_SRR4235089
## Number of contigs is 1163. Cumulated length is 35.05Mb.
## STnnJGI_SRR4235090
## Number of contigs is 957. Cumulated length is 35.67Mb.
## STnnJGI_SRR4235091
## Number of contigs is 1027. Cumulated length is 35.11Mb.
## STnnJGI_SRR4235092
## Number of contigs is 883. Cumulated length is 34.52Mb.
## STnnJGI_SRR4235093
## Number of contigs is 1045. Cumulated length is 35.2Mb.
## STnnJGI_SRR4235094
## Number of contigs is 1476. Cumulated length is 34.83Mb.
## STnnJGI_SRR4235095
## Number of contigs is 980. Cumulated length is 35.06Mb.
## STnnJGI_SRR4235096
## Number of contigs is 1122. Cumulated length is 34.38Mb.
## STnnJGI_SRR4235097
## Number of contigs is 1224. Cumulated length is 35.47Mb.
## STnnJGI_SRR4235098
## Number of contigs is 1024. Cumulated length is 34.94Mb.
## STnnJGI_SRR4235099
## Number of contigs is 1270. Cumulated length is 35.5Mb.
## STnnJGI_SRR4235100
## Number of contigs is 1091. Cumulated length is 34.89Mb.
## STnnJGI_SRR4235101
## Number of contigs is 1046. Cumulated length is 35.01Mb.
## STnnJGI_SRR4235102
## Number of contigs is 933. Cumulated length is 35.49Mb.
## STnnJGI_SRR4235103
## Number of contigs is 1163. Cumulated length is 35.2Mb.
## STnnJGI_SRR4235104
## Number of contigs is 1081. Cumulated length is 35.03Mb.
## STnnJGI_SRR4235106
## Number of contigs is 836. Cumulated length is 35.14Mb.
## STnnJGI_SRR4235107
## Number of contigs is 879. Cumulated length is 33.53Mb.
## STnnJGI_SRR4235108
## Number of contigs is 782. Cumulated length is 34.52Mb.
## STnnJGI_SRR4235110
## Number of contigs is 908. Cumulated length is 35.13Mb.
## STnnJGI_SRR4235111
## Number of contigs is 1016. Cumulated length is 35.9Mb.
## STnnJGI_SRR4235113
## Number of contigs is 987. Cumulated length is 35.82Mb.
## STnnJGI_SRR5194475
## Number of contigs is 679. Cumulated length is 35.57Mb.
## STnnJGI_SRR5194476
## Number of contigs is 799. Cumulated length is 36.21Mb.
## STnnJGI_SRR5194477
## Number of contigs is 705. Cumulated length is 36.75Mb.
## STnnJGI_SRR5194479
## Number of contigs is 564. Cumulated length is 35.01Mb.
## STnnJGI_SRR5194481
## Number of contigs is 734. Cumulated length is 36.13Mb.
## STnnJGI_SRR5194482
## Number of contigs is 834. Cumulated length is 35.92Mb.
## STnnJGI_SRR5194483
## Number of contigs is 775. Cumulated length is 35.5Mb.
## STnnJGI_SRR5194515
## Number of contigs is 718. Cumulated length is 36.21Mb.
## STnnJGI_SRR5194532
## Number of contigs is 572. Cumulated length is 33.73Mb.
## STnnJGI_SRR5194533
## Number of contigs is 725. Cumulated length is 34.51Mb.
## STnnJGI_SRR5194534
## Number of contigs is 585. Cumulated length is 35.91Mb.
## STnnJGI_SRR5194535
## Number of contigs is 621. Cumulated length is 35.05Mb.
## STnnJGI_SRR5194587
## Number of contigs is 647. Cumulated length is 34.48Mb.
## STnnJGI_SRR5194588
## Number of contigs is 764. Cumulated length is 35.59Mb.
## STnnJGI_SRR5194589
## Number of contigs is 683. Cumulated length is 35.36Mb.
## STnnJGI_SRR5194590
## Number of contigs is 534. Cumulated length is 34.37Mb.
## STnnJGI_SRR5194591
## Number of contigs is 658. Cumulated length is 35.36Mb.
## STnnJGI_SRR5194592
## Number of contigs is 700. Cumulated length is 35.62Mb.
## STnnJGI_SRR5194593
## Number of contigs is 609. Cumulated length is 35.82Mb.
## STnnJGI_SRR5194594
## Number of contigs is 664. Cumulated length is 35.83Mb.
## STnnJGI_SRR5194595
## Number of contigs is 539. Cumulated length is 34.18Mb.
## STnnJGI_SRR5194596
## Number of contigs is 732. Cumulated length is 35.69Mb.
## STnnJGI_SRR5194605
## Number of contigs is 705. Cumulated length is 35.84Mb.
## STnnJGI_SRR5194606
## Number of contigs is 1213. Cumulated length is 54.06Mb.
## STnnJGI_SRR5194607
## Number of contigs is 590. Cumulated length is 34.75Mb.
## STnnJGI_SRR5829643
## Number of contigs is 559. Cumulated length is 37.53Mb.
## STnnJGI_SRR5829673
## Number of contigs is 503. Cumulated length is 37.92Mb.
## STnnJGI_SRR5829674
## Number of contigs is 516. Cumulated length is 36.88Mb.
## STnnJGI_SRR5829692
## Number of contigs is 534. Cumulated length is 37.89Mb.
## STnnJGI_SRR6447858
## Number of contigs is 838. Cumulated length is 36.09Mb.
## STnnJGI_SRR6830963
## Number of contigs is 733. Cumulated length is 36.21Mb.
## STnnJGI_SRR6830964
## Number of contigs is 824. Cumulated length is 36.29Mb.
## STnnJGI_SRR6830965
## Number of contigs is 808. Cumulated length is 36.04Mb.
## STnnJGI_SRR6830966
## Number of contigs is 669. Cumulated length is 35.68Mb.
## STnnJGI_SRR6830967
## Number of contigs is 691. Cumulated length is 35.84Mb.
## STnnJGI_SRR6830968
## Number of contigs is 647. Cumulated length is 35.26Mb.
## STnnJGI_SRR6830969
## Number of contigs is 611. Cumulated length is 35.37Mb.
## STnnJGI_SRR6830970
## Number of contigs is 523. Cumulated length is 34.37Mb.
## STnnJGI_SRR6830971
## Number of contigs is 600. Cumulated length is 33.83Mb.
## STnnJGI_SRR6831004
## Number of contigs is 641. Cumulated length is 36.19Mb.
## STnnJGI_SRR6831008
## Number of contigs is 706. Cumulated length is 36.11Mb.
## STnnJGI_SRR6831009
## Number of contigs is 652. Cumulated length is 35.95Mb.
## STnnJGI_SRR6831010
## Number of contigs is 629. Cumulated length is 33.98Mb.
## STnnJGI_SRR6831056
## Number of contigs is 728. Cumulated length is 35.71Mb.
## STnnJGI_SRR7073263
## Number of contigs is 760. Cumulated length is 36.5Mb.
## STnnJGI_SRR7073288
## Number of contigs is 779. Cumulated length is 35.69Mb.
## STnnJGI_SRR7073289
## Number of contigs is 733. Cumulated length is 35.85Mb.
## STnnJGI_SRR7073427
## Number of contigs is 697. Cumulated length is 35.69Mb.
## STnnJGI_SRR7073430
## Number of contigs is 677. Cumulated length is 35.06Mb.
## STnnJGI_SRR7073431
## Number of contigs is 851. Cumulated length is 35.83Mb.
## STnnJGI_SRR7073594
## Number of contigs is 763. Cumulated length is 36.22Mb.
## STnnJGI_SRR7073614
## Number of contigs is 743. Cumulated length is 35.24Mb.
## STnnJGI_SRR7074464
## Number of contigs is 588. Cumulated length is 34.17Mb.
## STnnJGI_SRR7074626
## Number of contigs is 789. Cumulated length is 36.75Mb.
## STnnJGI_SRR7074627
## Number of contigs is 844. Cumulated length is 36.48Mb.
## Switzerland_1999_ST99CH_3B6
## Number of contigs is 1113. Cumulated length is 36.29Mb.
## Switzerland_1999_ST99CH_3C9
## Number of contigs is 1225. Cumulated length is 34.72Mb.
## Syria_1992_SYK2
## Number of contigs is 1025. Cumulated length is 35.94Mb.
## Syria_1992_SYK3
## Number of contigs is 884. Cumulated length is 35.69Mb.
## Syria_1992_SYK4
## Number of contigs is 1018. Cumulated length is 35.67Mb.
## Syria_1992_SYT2
## Number of contigs is 956. Cumulated length is 35.53Mb.
## Syria_1992_SYT3
## Number of contigs is 955. Cumulated length is 35.7Mb.
## Texas_1994_ST94TX_PA2a_1
## Number of contigs is 1019. Cumulated length is 35.59Mb.
## Texas_1994_ST94TX_PB2a_1
## Number of contigs is 1021. Cumulated length is 34.17Mb.
## Texas_1994_ST94TX_PB3a_1
## Number of contigs is 1266. Cumulated length is 35.97Mb.
## Texas_1994_ST94TX_PB4a_1
## Number of contigs is 1057. Cumulated length is 35.3Mb.
## Texas_1994_ST94TX_PC2a_1
## Number of contigs is 1229. Cumulated length is 36.03Mb.
## Texas_1994_ST94TX_PC3a_1
## Number of contigs is 1099. Cumulated length is 35.48Mb.
## Texas_1994_ST94TX_PD1a_1
## Number of contigs is 1203. Cumulated length is 35.34Mb.
## Texas_1994_ST94TX_PD4a_1
## Number of contigs is 1126. Cumulated length is 35.26Mb.
## Texas_1994_ST94TX_PF4a_1
## Number of contigs is 5514. Cumulated length is 28.66Mb.
## Texas_1995_ST94TX_PG3a_1
## Number of contigs is 1202. Cumulated length is 35.67Mb.
## Tunisia_2008_ST08TN_33_1_2
## Number of contigs is 139. Cumulated length is 12.7Mb.
## Tunisia_2008_ST08TN_33_4_3
## Number of contigs is 1029. Cumulated length is 34.82Mb.
## Tunisia_2008_ST08TN_33_4_9
## Number of contigs is 1114. Cumulated length is 35.31Mb.
## Tunisia_2008_ST08TN_33_5_8
## Number of contigs is 1189. Cumulated length is 35.9Mb.
## Tunisia_2008_ST08TN_33_6_2
## Number of contigs is 1186. Cumulated length is 34.5Mb.
## Tunisia_2008_ST08TN_33_6_6
## Number of contigs is 1096. Cumulated length is 34.32Mb.
## Tunisia_2008_ST08TN_33_6_9
## Number of contigs is 1248. Cumulated length is 36.15Mb.
## Tunisia_2008_ST08TN_33_7_4
## Number of contigs is 1214. Cumulated length is 36.0Mb.
## Tunisia_2008_ST08TN_33_8_4
## Number of contigs is 1164. Cumulated length is 35.44Mb.
## Tunisia_2008_ST08TN_33_8_7
## Number of contigs is 1066. Cumulated length is 34.82Mb.
## Tunisia_2008_ST08TN_33_8_9
## Number of contigs is 1144. Cumulated length is 35.44Mb.
## Tunisia_2008_ST08TN_33_9_6
## Number of contigs is 1017. Cumulated length is 35.73Mb.
## Turkey_1992_TKA1a
## Number of contigs is 1075. Cumulated length is 34.94Mb.
## Turkey_1992_TKA1b
## Number of contigs is 1068. Cumulated length is 34.85Mb.
## Turkey_1992_TKA2a
## Number of contigs is 1004. Cumulated length is 34.75Mb.
## Turkey_1992_TKA2c
## Number of contigs is 1058. Cumulated length is 35.54Mb.
## Turkey_1992_TKV1
## Number of contigs is 1407. Cumulated length is 35.91Mb.
## Turkey_1992_TKV2a
## Number of contigs is 1121. Cumulated length is 35.77Mb.
## Turkey_1992_TKV2b
## Number of contigs is 961. Cumulated length is 36.27Mb.
## Ukraine_1995_ST95UR_BIc_1
## Number of contigs is 1582. Cumulated length is 36.07Mb.
## Ukraine_1995_ST95UR_E2a_1
## Number of contigs is 1185. Cumulated length is 34.83Mb.
## Ukraine_1995_ST95UR_E2c_2
## Number of contigs is 1155. Cumulated length is 34.99Mb.
## Ukraine_1995_ST95UR_F1a_1
## Number of contigs is 1407. Cumulated length is 34.97Mb.
## Ukraine_1995_ST95UR_F1a_3
## Number of contigs is 1285. Cumulated length is 36.08Mb.
## Ukraine_1995_ST95UR_F1c_2
## Number of contigs is 1175. Cumulated length is 36.37Mb.
## Ukraine_1995_ST95UR_F2a_1
## Number of contigs is 1287. Cumulated length is 35.81Mb.
## Uruguay_1993_STUR93_EC1b_1
## Number of contigs is 1218. Cumulated length is 35.92Mb.
## Uruguay_1993_STUR93_EC1c_1
## Number of contigs is 1257. Cumulated length is 36.45Mb.
## Uruguay_1993_STUR93_EC2b_1
## Number of contigs is 1192. Cumulated length is 36.68Mb.
## Uruguay_1993_STUR93_EC3d_1
## Number of contigs is 1287. Cumulated length is 34.99Mb.
## Uruguay_1993_STUR93_ED3b_1
## Number of contigs is 728. Cumulated length is 34.94Mb.
## Uruguay_1993_STUR93_EE1d_1
## Number of contigs is 1239. Cumulated length is 36.2Mb.
## Uruguay_1993_STUR93_EE2a_1
## Number of contigs is 1220. Cumulated length is 36.64Mb.
## Uruguay_1993_STUR93_EE3a_1
## Number of contigs is 1199. Cumulated length is 35.96Mb.
## Uruguay_1993_STUR93_EG4a_3
## Number of contigs is 1166. Cumulated length is 36.02Mb.
## Uruguay_1993_STUR93_EG4c_1
## Number of contigs is 1133. Cumulated length is 36.61Mb.
## Uruguay_1993_STUR93_LA4a_1
## Number of contigs is 1044. Cumulated length is 36.14Mb.
## Uruguay_1993_STUR93_LC1b_1
## Number of contigs is 1123. Cumulated length is 35.73Mb.
## Uruguay_1993_STUR93_LF2b_1
## Number of contigs is 1183. Cumulated length is 36.77Mb.
## Uruguay_1993_STUR93_LH4a_1
## Number of contigs is 1265. Cumulated length is 36.05Mb.
## Yemen_1992_YEQ2
## Number of contigs is 980. Cumulated length is 35.71Mb.
## Yemen_1992_YEQ4
## Number of contigs is 1096. Cumulated length is 35.44Mb.
## 05STB001_1
## Number of contigs is 29521. Cumulated length is 41.19Mb.
## 05STB003_1
## Number of contigs is 30871. Cumulated length is 41.66Mb.
## 05STB011_1
## Number of contigs is 26695. Cumulated length is 40.69Mb.
## 05STB012_1
## Number of contigs is 27458. Cumulated length is 41.5Mb.
## 05STB013_1
## Number of contigs is 23983. Cumulated length is 39.42Mb.
## 05STB015_1
## Number of contigs is 39065. Cumulated length is 41.82Mb.
## 05STB017_1
## Number of contigs is 43306. Cumulated length is 44.45Mb.
## 05STB023_1
## Number of contigs is 27531. Cumulated length is 40.49Mb.
## 05STB026_1
## Number of contigs is 28086. Cumulated length is 41.31Mb.
## 05STB028_1
## Number of contigs is 26112. Cumulated length is 40.37Mb.
## 05STCH001_1
## Number of contigs is 30395. Cumulated length is 41.65Mb.
## 05STCH002_1
## Number of contigs is 41614. Cumulated length is 41.55Mb.
## 05STCH003_1
## Number of contigs is 31206. Cumulated length is 41.11Mb.
## 05STCH004_1
## Number of contigs is 26960. Cumulated length is 39.96Mb.
## 05STCH008_1
## Number of contigs is 26961. Cumulated length is 40.07Mb.
## 05STD001_1
## Number of contigs is 29229. Cumulated length is 41.75Mb.
## 05STD006_1
## Number of contigs is 26777. Cumulated length is 40.73Mb.
## 05STD026_1
## Number of contigs is 33749. Cumulated length is 40.11Mb.
## 05STD031_1
## Number of contigs is 24926. Cumulated length is 40.44Mb.
## 05STD040_1
## Number of contigs is 27757. Cumulated length is 40.9Mb.
## 05STD041_1
## Number of contigs is 27960. Cumulated length is 40.46Mb.
## 05STD042_1
## Number of contigs is 30187. Cumulated length is 41.62Mb.
## 05STD046_1
## Number of contigs is 26362. Cumulated length is 39.51Mb.
## 05STD059_1
## Number of contigs is 30329. Cumulated length is 41.41Mb.
## 05STD069_1
## Number of contigs is 24191. Cumulated length is 40.43Mb.
## 05STD087_1
## Number of contigs is 27216. Cumulated length is 40.54Mb.
## 05STD093_1
## Number of contigs is 28367. Cumulated length is 40.12Mb.
## 05STD094_1
## Number of contigs is 26464. Cumulated length is 40.57Mb.
## 05STD098_1
## Number of contigs is 26451. Cumulated length is 40.22Mb.
## 05STD104_1
## Number of contigs is 31400. Cumulated length is 40.8Mb.
## 05STD108_1
## Number of contigs is 29430. Cumulated length is 41.7Mb.
## 05STD127_1
## Number of contigs is 29391. Cumulated length is 40.76Mb.
## 05STD133_1
## Number of contigs is 39991. Cumulated length is 42.3Mb.
## 05STD138_1
## Number of contigs is 29946. Cumulated length is 41.19Mb.
## 05STIR001
## Number of contigs is 24622. Cumulated length is 39.44Mb.
## 05STNL002_1
## Number of contigs is 33728. Cumulated length is 41.5Mb.
## 05STNL003_1
## Number of contigs is 27603. Cumulated length is 40.75Mb.
## 05STNL015_1
## Number of contigs is 27774. Cumulated length is 41.22Mb.
## 05STNL024_1
## Number of contigs is 25837. Cumulated length is 40.04Mb.
## 05STPL002_1
## Number of contigs is 23368. Cumulated length is 39.35Mb.
## 05STPL003_1
## Number of contigs is 22555. Cumulated length is 39.25Mb.
## 05STPL005_1
## Number of contigs is 40730. Cumulated length is 44.9Mb.
## 05STPL007_1
## Number of contigs is 31947. Cumulated length is 41.71Mb.
## 05STPL008_1
## Number of contigs is 29101. Cumulated length is 42.56Mb.
## 06STCZ001
## Number of contigs is 31100. Cumulated length is 41.65Mb.
## 06STCZ003
## Number of contigs is 29316. Cumulated length is 40.71Mb.
## 06STCZ007
## Number of contigs is 33969. Cumulated length is 41.78Mb.
## 06STCZ009
## Number of contigs is 36469. Cumulated length is 41.78Mb.
## 06STCZ016
## Number of contigs is 26492. Cumulated length is 40.33Mb.
## 06STCZ020
## Number of contigs is 28724. Cumulated length is 40.32Mb.
## 06STCZ023
## Number of contigs is 26023. Cumulated length is 40.08Mb.
## 06STCZ028
## Number of contigs is 30187. Cumulated length is 40.68Mb.
## 06STCZ036
## Number of contigs is 25819. Cumulated length is 40.26Mb.
## 06STCZ044
## Number of contigs is 40839. Cumulated length is 42.46Mb.
## 06STCZ045
## Number of contigs is 35317. Cumulated length is 42.2Mb.
## 06STD024
## Number of contigs is 34590. Cumulated length is 44.33Mb.
## 06STGB002
## Number of contigs is 23356. Cumulated length is 40.13Mb.
## 06STGB003
## Number of contigs is 24933. Cumulated length is 39.82Mb.
## 06STGB006
## Number of contigs is 21113. Cumulated length is 39.36Mb.
## 06STGB013
## Number of contigs is 23080. Cumulated length is 40.36Mb.
## 06STGB015
## Number of contigs is 25966. Cumulated length is 40.42Mb.
## 06STGB018
## Number of contigs is 26408. Cumulated length is 40.51Mb.
## 06STGB020
## Number of contigs is 27397. Cumulated length is 40.89Mb.
## 06STIR001
## Number of contigs is 26487. Cumulated length is 40.6Mb.
## 06STIR002
## Number of contigs is 31126. Cumulated length is 41.14Mb.
## 06STIR003
## Number of contigs is 21619. Cumulated length is 36.82Mb.
## 06STIR004
## Number of contigs is 37034. Cumulated length is 42.03Mb.
## 06STIR005
## Number of contigs is 32678. Cumulated length is 41.16Mb.
## 06STIR008
## Number of contigs is 25031. Cumulated length is 39.84Mb.
## 07STF011
## Number of contigs is 27539. Cumulated length is 41.53Mb.
## 07STF021
## Number of contigs is 23539. Cumulated length is 39.55Mb.
## 07STF031
## Number of contigs is 32025. Cumulated length is 41.92Mb.
## 07STF041
## Number of contigs is 31887. Cumulated length is 41.04Mb.
## 07STF051
## Number of contigs is 25125. Cumulated length is 40.0Mb.
## 07STF058
## Number of contigs is 32982. Cumulated length is 42.25Mb.
## 07STF094
## Number of contigs is 27208. Cumulated length is 40.83Mb.
## 07STF104
## Number of contigs is 21654. Cumulated length is 38.89Mb.
## 07STF145
## Number of contigs is 38049. Cumulated length is 42.18Mb.
## 07STF146
## Number of contigs is 28443. Cumulated length is 41.07Mb.
## 07STF148
## Number of contigs is 36336. Cumulated length is 41.75Mb.
## 07STF160
## Number of contigs is 27084. Cumulated length is 40.71Mb.
## 07STF190
## Number of contigs is 22557. Cumulated length is 39.29Mb.
## 07STGB009
## Number of contigs is 30009. Cumulated length is 41.87Mb.
## 08STB003
## Number of contigs is 27484. Cumulated length is 40.51Mb.
## 08STB009
## Number of contigs is 29933. Cumulated length is 39.93Mb.
## 08STB010
## Number of contigs is 30088. Cumulated length is 40.73Mb.
## 08STB011
## Number of contigs is 27889. Cumulated length is 39.42Mb.
## 08STCH005
## Number of contigs is 22786. Cumulated length is 39.59Mb.
## 08STCH007
## Number of contigs is 26337. Cumulated length is 40.74Mb.
## 08STCH008
## Number of contigs is 35567. Cumulated length is 41.28Mb.
## 08STCH015
## Number of contigs is 35336. Cumulated length is 42.35Mb.
## 08STCZ003
## Number of contigs is 30552. Cumulated length is 41.41Mb.
## 08STCZ004
## Number of contigs is 31308. Cumulated length is 42.04Mb.
## 08STCZ010
## Number of contigs is 31563. Cumulated length is 41.65Mb.
## 08STCZ011
## Number of contigs is 43326. Cumulated length is 48.87Mb.
## 08STCZ015
## Number of contigs is 29833. Cumulated length is 40.53Mb.
## 08STCZ016
## Number of contigs is 31454. Cumulated length is 41.85Mb.
## 08STCZ023
## Number of contigs is 28701. Cumulated length is 40.8Mb.
## 08STD013
## Number of contigs is 25892. Cumulated length is 40.16Mb.
## 08STD016
## Number of contigs is 26476. Cumulated length is 40.56Mb.
## 08STD018
## Number of contigs is 27914. Cumulated length is 40.98Mb.
## 08STD019
## Number of contigs is 29769. Cumulated length is 41.29Mb.
## 08STD020
## Number of contigs is 20572. Cumulated length is 39.8Mb.
## 08STD021
## Number of contigs is 29700. Cumulated length is 40.84Mb.
## 08STD022
## Number of contigs is 29760. Cumulated length is 40.7Mb.
## 08STD045
## Number of contigs is 31287. Cumulated length is 41.22Mb.
## 08STD046
## Number of contigs is 31336. Cumulated length is 41.21Mb.
## 08STF006
## Number of contigs is 35622. Cumulated length is 41.77Mb.
## 08STF029
## Number of contigs is 29859. Cumulated length is 40.54Mb.
## 08STF030
## Number of contigs is 30311. Cumulated length is 40.65Mb.
## 08STF034
## Number of contigs is 25592. Cumulated length is 38.75Mb.
## 08STF035
## Number of contigs is 26127. Cumulated length is 40.17Mb.
## 08STF036
## Number of contigs is 22957. Cumulated length is 38.99Mb.
## 08STF040
## Number of contigs is 31191. Cumulated length is 41.18Mb.
## 08STF048
## Number of contigs is 30924. Cumulated length is 41.73Mb.
## 08STF051
## Number of contigs is 27955. Cumulated length is 39.99Mb.
## 08STF052
## Number of contigs is 28544. Cumulated length is 40.23Mb.
## 08STF056
## Number of contigs is 36139. Cumulated length is 42.46Mb.
## 08STF063
## Number of contigs is 32543. Cumulated length is 42.2Mb.
## 08STF070
## Number of contigs is 32635. Cumulated length is 40.85Mb.
## 08STF076
## Number of contigs is 29137. Cumulated length is 40.81Mb.
## 08STF077
## Number of contigs is 28458. Cumulated length is 40.58Mb.
## 08STF078
## Number of contigs is 28822. Cumulated length is 41.28Mb.
## 08STF079
## Number of contigs is 27636. Cumulated length is 40.83Mb.
## 08STF082
## Number of contigs is 30038. Cumulated length is 40.47Mb.
## 08STF083
## Number of contigs is 34413. Cumulated length is 41.32Mb.
## 08STF089
## Number of contigs is 30565. Cumulated length is 41.01Mb.
## 08STF094
## Number of contigs is 35791. Cumulated length is 42.22Mb.
## 08STF098
## Number of contigs is 26156. Cumulated length is 40.43Mb.
## 08STF102
## Number of contigs is 33529. Cumulated length is 41.68Mb.
## 08STF105
## Number of contigs is 27370. Cumulated length is 40.22Mb.
## 08STF106
## Number of contigs is 32679. Cumulated length is 40.81Mb.
## 08STF108
## Number of contigs is 24488. Cumulated length is 38.36Mb.
## 08STF109
## Number of contigs is 25805. Cumulated length is 39.42Mb.
## 08STF116
## Number of contigs is 29741. Cumulated length is 40.57Mb.
## 08STF128
## Number of contigs is 24658. Cumulated length is 39.78Mb.
## 08STF131
## Number of contigs is 31765. Cumulated length is 40.93Mb.
## 08STF136
## Number of contigs is 21920. Cumulated length is 38.73Mb.
## 08STF147
## Number of contigs is 34558. Cumulated length is 40.74Mb.
## 08STF153
## Number of contigs is 33227. Cumulated length is 41.79Mb.
## 08STF155
## Number of contigs is 32303. Cumulated length is 41.11Mb.
## 08STF175
## Number of contigs is 26896. Cumulated length is 39.99Mb.
## 08STF183
## Number of contigs is 28991. Cumulated length is 41.08Mb.
## 08STF185
## Number of contigs is 33569. Cumulated length is 41.72Mb.
## 08STF187
## Number of contigs is 32618. Cumulated length is 41.56Mb.
## 08STF194
## Number of contigs is 23056. Cumulated length is 38.18Mb.
## 08STF196
## Number of contigs is 24641. Cumulated length is 38.94Mb.
## 08STGB001
## Number of contigs is 26874. Cumulated length is 40.15Mb.
## 08STGB003
## Number of contigs is 35592. Cumulated length is 42.15Mb.
## 08STGB004
## Number of contigs is 28300. Cumulated length is 40.93Mb.
## 08STGB006
## Number of contigs is 30656. Cumulated length is 41.02Mb.
## 08STGB007
## Number of contigs is 35038. Cumulated length is 42.02Mb.
## 09STD003
## Number of contigs is 27191. Cumulated length is 40.77Mb.
## 09STD004
## Number of contigs is 30682. Cumulated length is 40.87Mb.
## 09STD007
## Number of contigs is 24536. Cumulated length is 39.9Mb.
## 09STD019
## Number of contigs is 44513. Cumulated length is 41.86Mb.
## 09STD024
## Number of contigs is 27517. Cumulated length is 41.58Mb.
## 09STD031
## Number of contigs is 29176. Cumulated length is 40.35Mb.
## 09STD041
## Number of contigs is 29478. Cumulated length is 41.31Mb.
## 09STD044
## Number of contigs is 19906. Cumulated length is 40.62Mb.
## 09STD053
## Number of contigs is 34271. Cumulated length is 42.01Mb.
## 09STD054
## Number of contigs is 36550. Cumulated length is 41.46Mb.
## 09STD057
## Number of contigs is 19971. Cumulated length is 38.25Mb.
## 09STD059
## Number of contigs is 27852. Cumulated length is 40.48Mb.
## 09STD061
## Number of contigs is 33692. Cumulated length is 40.49Mb.
## 09STD062
## Number of contigs is 28596. Cumulated length is 40.78Mb.
## 09STD070
## Number of contigs is 29978. Cumulated length is 40.34Mb.
## 09STD071
## Number of contigs is 41875. Cumulated length is 42.08Mb.
## 09STD072
## Number of contigs is 46427. Cumulated length is 42.67Mb.
## 09STD073
## Number of contigs is 33062. Cumulated length is 41.29Mb.
## 09STD074
## Number of contigs is 43232. Cumulated length is 40.95Mb.
## 09STD075
## Number of contigs is 34194. Cumulated length is 40.77Mb.
## 09STD076
## Number of contigs is 20217. Cumulated length is 41.08Mb.
## 09STD077
## Number of contigs is 28755. Cumulated length is 40.03Mb.
## 09STD078
## Number of contigs is 30868. Cumulated length is 41.09Mb.
## 09STD079
## Number of contigs is 27470. Cumulated length is 41.02Mb.
## 09STE001
## Number of contigs is 57252. Cumulated length is 44.38Mb.
## 09STE002
## Number of contigs is 60751. Cumulated length is 45.25Mb.
## 09STF004
## Number of contigs is 27982. Cumulated length is 41.17Mb.
## 09STF005
## Number of contigs is 28352. Cumulated length is 39.51Mb.
## 09STF007
## Number of contigs is 35057. Cumulated length is 41.09Mb.
## 09STF011
## Number of contigs is 32595. Cumulated length is 40.12Mb.
## 09STF013
## Number of contigs is 23816. Cumulated length is 39.11Mb.
## 09STF014
## Number of contigs is 36857. Cumulated length is 40.6Mb.
## 09STF015
## Number of contigs is 43718. Cumulated length is 42.22Mb.
## 09STF019
## Number of contigs is 51047. Cumulated length is 42.6Mb.
## 09STF024
## Number of contigs is 18897. Cumulated length is 40.65Mb.
## 09STF025
## Number of contigs is 27956. Cumulated length is 40.82Mb.
## 09STF027
## Number of contigs is 47177. Cumulated length is 47.54Mb.
## 09STF028
## Number of contigs is 44928. Cumulated length is 41.56Mb.
## 09STF029
## Number of contigs is 28887. Cumulated length is 38.34Mb.
## 09STF031
## Number of contigs is 37056. Cumulated length is 44.07Mb.
## 09STF032
## Number of contigs is 41168. Cumulated length is 44.57Mb.
## 09STF036
## Number of contigs is 24795. Cumulated length is 40.78Mb.
## 09STF037
## Number of contigs is 30522. Cumulated length is 41.9Mb.
## 09STF045
## Number of contigs is 35792. Cumulated length is 42.35Mb.
## 09STF046
## Number of contigs is 34056. Cumulated length is 41.67Mb.
## 09STF048
## Number of contigs is 22828. Cumulated length is 40.36Mb.
## 09STF054
## Number of contigs is 25382. Cumulated length is 40.87Mb.
## 09STF056
## Number of contigs is 25204. Cumulated length is 40.19Mb.
## 09STF058
## Number of contigs is 20684. Cumulated length is 39.01Mb.
## 09STF063
## Number of contigs is 25292. Cumulated length is 40.3Mb.
## 09STF068
## Number of contigs is 34713. Cumulated length is 42.84Mb.
## 09STF077
## Number of contigs is 40029. Cumulated length is 41.51Mb.
## 09STF079
## Number of contigs is 40212. Cumulated length is 41.73Mb.
## 09STF081
## Number of contigs is 25418. Cumulated length is 39.47Mb.
## 09STF082
## Number of contigs is 40250. Cumulated length is 42.06Mb.
## 09STF094
## Number of contigs is 30274. Cumulated length is 39.7Mb.
## 09STF096
## Number of contigs is 21301. Cumulated length is 39.87Mb.
## 09STF097
## Number of contigs is 21215. Cumulated length is 39.45Mb.
## 09STF098
## Number of contigs is 21561. Cumulated length is 40.37Mb.
## 09STF099
## Number of contigs is 26664. Cumulated length is 40.57Mb.
## 09STF103
## Number of contigs is 34765. Cumulated length is 42.2Mb.
## 09STF105
## Number of contigs is 20041. Cumulated length is 38.83Mb.
## 09STF106
## Number of contigs is 20924. Cumulated length is 40.27Mb.
## 09STF109
## Number of contigs is 36893. Cumulated length is 41.16Mb.
## 09STF112
## Number of contigs is 40168. Cumulated length is 42.53Mb.
## 09STF114
## Number of contigs is 23961. Cumulated length is 40.38Mb.
## 09STGB001
## Number of contigs is 18073. Cumulated length is 38.48Mb.
## 09STGB002
## Number of contigs is 33772. Cumulated length is 40.95Mb.
## 09STGB004
## Number of contigs is 16406. Cumulated length is 39.18Mb.
## 09STIR003_1
## Number of contigs is 31983. Cumulated length is 41.57Mb.
## 09STIR004_2
## Number of contigs is 30936. Cumulated length is 40.4Mb.
## 09STIR005_2
## Number of contigs is 28652. Cumulated length is 40.34Mb.
## 09STIR007_3
## Number of contigs is 20040. Cumulated length is 39.86Mb.
## 09STIR009_5
## Number of contigs is 37789. Cumulated length is 41.21Mb.
## 09STIR010_4
## Number of contigs is 21151. Cumulated length is 41.43Mb.
## 09STIR012_3
## Number of contigs is 21457. Cumulated length is 40.26Mb.
## 09STIR013_1
## Number of contigs is 17388. Cumulated length is 37.83Mb.
## 09STIR014_1
## Number of contigs is 28188. Cumulated length is 41.69Mb.
## 09STIR014_3
## Number of contigs is 35219. Cumulated length is 41.88Mb.
## 09STIR015_1
## Number of contigs is 25798. Cumulated length is 37.38Mb.
## 09STIR016_2
## Number of contigs is 28167. Cumulated length is 40.79Mb.
## 09STIR016_3
## Number of contigs is 28939. Cumulated length is 39.78Mb.
## 09STIR017_5
## Number of contigs is 24126. Cumulated length is 40.04Mb.
## 09STIR018_1
## Number of contigs is 27993. Cumulated length is 40.86Mb.
## 09STIR019_4
## Number of contigs is 35268. Cumulated length is 41.83Mb.
## 09STIR020_1
## Number of contigs is 24763. Cumulated length is 40.34Mb.
## 09STIR020_3
## Number of contigs is 19256. Cumulated length is 39.95Mb.
## 09STIR021_2
## Number of contigs is 32296. Cumulated length is 41.8Mb.
## 09STIR022_1
## Number of contigs is 24466. Cumulated length is 40.54Mb.
## 09STIR022_4
## Number of contigs is 26160. Cumulated length is 41.21Mb.
## 09STIR023_3
## Number of contigs is 27725. Cumulated length is 40.77Mb.
## 09STIR024_2
## Number of contigs is 26016. Cumulated length is 40.67Mb.
## 09STIR026_2
## Number of contigs is 33597. Cumulated length is 44.73Mb.
## 09STIR026_4
## Number of contigs is 17545. Cumulated length is 37.99Mb.
## 09STIR026_5
## Number of contigs is 19546. Cumulated length is 38.09Mb.
## 09STIR027_3
## Number of contigs is 17566. Cumulated length is 38.12Mb.
## 09STIR027_5
## Number of contigs is 30042. Cumulated length is 41.08Mb.
## 10STBY001
## Number of contigs is 33165. Cumulated length is 40.31Mb.
## 10STD001
## Number of contigs is 31086. Cumulated length is 41.48Mb.
## 10STD002
## Number of contigs is 42164. Cumulated length is 45.73Mb.
## 10STD017
## Number of contigs is 27178. Cumulated length is 39.94Mb.
## 10STD019
## Number of contigs is 34049. Cumulated length is 41.92Mb.
## 10STDK003
## Number of contigs is 26720. Cumulated length is 40.54Mb.
## 10STF023
## Number of contigs is 28497. Cumulated length is 39.77Mb.
## 10STF036
## Number of contigs is 32288. Cumulated length is 40.39Mb.
## 10STF049
## Number of contigs is 30172. Cumulated length is 40.85Mb.
## 10STF057
## Number of contigs is 28020. Cumulated length is 41.03Mb.
## 10STF058
## Number of contigs is 30378. Cumulated length is 40.93Mb.
## 10STF078
## Number of contigs is 36916. Cumulated length is 42.55Mb.
## 10STF082
## Number of contigs is 34585. Cumulated length is 41.78Mb.
## 10STF146
## Number of contigs is 31957. Cumulated length is 41.25Mb.
## 10STF150
## Number of contigs is 29321. Cumulated length is 40.72Mb.
## 10STF163
## Number of contigs is 31514. Cumulated length is 40.88Mb.
## 10STF164
## Number of contigs is 35506. Cumulated length is 41.68Mb.
## 10STF178
## Number of contigs is 34672. Cumulated length is 42.37Mb.
## 10STF190
## Number of contigs is 32488. Cumulated length is 41.73Mb.
## 10STF202
## Number of contigs is 30565. Cumulated length is 40.8Mb.
## 10STF227
## Number of contigs is 38911. Cumulated length is 42.01Mb.
## 10STF231
## Number of contigs is 33365. Cumulated length is 41.56Mb.
## 10STF241
## Number of contigs is 29528. Cumulated length is 40.95Mb.
## 10STF248
## Number of contigs is 28822. Cumulated length is 39.69Mb.
## 10STF253
## Number of contigs is 24642. Cumulated length is 39.94Mb.
## 10STF261
## Number of contigs is 31514. Cumulated length is 41.52Mb.
## 10STGB007
## Number of contigs is 32798. Cumulated length is 41.54Mb.
## 10STGB015
## Number of contigs is 27713. Cumulated length is 40.59Mb.
## 10STGB024
## Number of contigs is 29346. Cumulated length is 40.99Mb.
## 10STGB025
## Number of contigs is 24199. Cumulated length is 39.91Mb.
## 10STGB031
## Number of contigs is 21533. Cumulated length is 38.31Mb.
## 10STGB035
## Number of contigs is 20629. Cumulated length is 38.69Mb.
## 10STGB036
## Number of contigs is 24913. Cumulated length is 40.42Mb.
## 10STGB037
## Number of contigs is 21217. Cumulated length is 38.0Mb.
## 10ST_Syn_D003
## Number of contigs is 34549. Cumulated length is 41.39Mb.
## 10ST_Syn_D005
## Number of contigs is 31507. Cumulated length is 41.02Mb.
## Algeria_1992_ALA1c
## Number of contigs is 97439. Cumulated length is 46.83Mb.
## Algeria_1992_ALA2a
## Number of contigs is 125606. Cumulated length is 49.53Mb.
## Algeria_1992_ALA3a
## Number of contigs is 58601. Cumulated length is 44.93Mb.
## Algeria_1992_ALG1a
## Number of contigs is 121268. Cumulated length is 50.76Mb.
## Algeria_1992_ALG1d
## Number of contigs is 111909. Cumulated length is 48.42Mb.
## Algeria_1992_ALG1e
## Number of contigs is 122014. Cumulated length is 51.51Mb.
## Argentina_2000_BOO10_F9a2
## Number of contigs is 39348. Cumulated length is 43.04Mb.
## Argentina_2000_BOO12_F5a1
## Number of contigs is 32869. Cumulated length is 42.7Mb.
## Argentina_2000_BOO14_F15a3
## Number of contigs is 45484. Cumulated length is 43.5Mb.
## Argentina_2000_BOO28_F15b2
## Number of contigs is 29362. Cumulated length is 41.59Mb.
## Argentina_2000_BOO32_B5a1
## Number of contigs is 29857. Cumulated length is 40.64Mb.
## Argentina_2000_BOO36_B4a1
## Number of contigs is 44392. Cumulated length is 42.9Mb.
## Argentina_2000_BOO54_F8b1
## Number of contigs is 37322. Cumulated length is 39.84Mb.
## Argentina_2000_BOO59_C4a2
## Number of contigs is 32287. Cumulated length is 40.49Mb.
## Argentina_2000_BOO61_FI5b2p
## Number of contigs is 26564. Cumulated length is 40.48Mb.
## Argentina_2000_BOO71_EI1a2p
## Number of contigs is 51619. Cumulated length is 46.29Mb.
## Argentina_2000_BOO9_F15a2
## Number of contigs is 41527. Cumulated length is 41.69Mb.
## California_1989_CB11A_ST1
## Number of contigs is 36292. Cumulated length is 40.19Mb.
## California_1989_CC22C_ST16
## Number of contigs is 32478. Cumulated length is 42.17Mb.
## California_1989_CE31B_ST42
## Number of contigs is 32884. Cumulated length is 41.6Mb.
## California_1989_CF11A_ST44
## Number of contigs is 30783. Cumulated length is 39.64Mb.
## California_1989_CF31C_ST52
## Number of contigs is 40598. Cumulated length is 40.64Mb.
## California_1989_CH33C_ST97
## Number of contigs is 33334. Cumulated length is 39.8Mb.
## Canada_1992_CNRA1a_1
## Number of contigs is 38003. Cumulated length is 42.63Mb.
## Canada_1992_CNRA4b_1
## Number of contigs is 34596. Cumulated length is 40.34Mb.
## Canada_1992_CNRB2b_4
## Number of contigs is 23776. Cumulated length is 37.63Mb.
## Canada_1992_CNRD4a_2
## Number of contigs is 42053. Cumulated length is 42.07Mb.
## Canada_1992_CNRE2a_2
## Number of contigs is 47311. Cumulated length is 45.05Mb.
## Canada_1992_CNRE4b_1
## Number of contigs is 41437. Cumulated length is 43.9Mb.
## Canada_1992_CNRG3a_1
## Number of contigs is 48724. Cumulated length is 45.64Mb.
## Canada_1992_CNRH3a_1
## Number of contigs is 32746. Cumulated length is 40.32Mb.
## Chile_1995_STCH95_10B4a
## Number of contigs is 31977. Cumulated length is 38.98Mb.
## Chile_1995_STCH95_1A2a
## Number of contigs is 41789. Cumulated length is 43.22Mb.
## Chile_1995_STCH95_1B1a
## Number of contigs is 37588. Cumulated length is 40.41Mb.
## Chile_1995_STCH95_1B2a
## Number of contigs is 31011. Cumulated length is 39.13Mb.
## Chile_1995_STCH95_1C3a
## Number of contigs is 37231. Cumulated length is 40.3Mb.
## Chile_1995_STCH95_1F2a
## Number of contigs is 24432. Cumulated length is 36.51Mb.
## Chile_1995_STCH95_1F3a
## Number of contigs is 33298. Cumulated length is 38.8Mb.
## Chile_1995_STCH95_1G3a
## Number of contigs is 25693. Cumulated length is 38.65Mb.
## Chile_1995_STCH95_1H1a
## Number of contigs is 30564. Cumulated length is 39.25Mb.
## Chile_1995_STCH95_1H2a
## Number of contigs is 38421. Cumulated length is 41.96Mb.
## Chile_1995_STCH95_3A3a
## Number of contigs is 36115. Cumulated length is 40.96Mb.
## Chile_1995_STCH95_3E4a
## Number of contigs is 34619. Cumulated length is 40.82Mb.
## Ethiopia_1992_ETD1
## Number of contigs is 127957. Cumulated length is 48.79Mb.
## Ethiopia_1992_ETK1
## Number of contigs is 40645. Cumulated length is 41.32Mb.
## Ethiopia_1992_ETK2a_1
## Number of contigs is 42947. Cumulated length is 41.49Mb.
## Ethiopia_1992_ETK2a_2
## Number of contigs is 52746. Cumulated length is 45.0Mb.
## Indiana_1993_I15a_1
## Number of contigs is 38198. Cumulated length is 42.97Mb.
## Indiana_1993_I1a_1
## Number of contigs is 48639. Cumulated length is 42.18Mb.
## Indiana_1993_I22a_1
## Number of contigs is 32665. Cumulated length is 41.01Mb.
## Indiana_1993_I24a_1
## Number of contigs is 24676. Cumulated length is 39.56Mb.
## Indiana_1993_I25a_1
## Number of contigs is 28371. Cumulated length is 39.66Mb.
## Indiana_1993_I31a_1
## Number of contigs is 35024. Cumulated length is 40.79Mb.
## Indiana_1993_I33a_1
## Number of contigs is 29421. Cumulated length is 39.41Mb.
## Indiana_1993_I9a_1
## Number of contigs is 33042. Cumulated length is 40.34Mb.
## Iran_2001_STIR01A13a
## Number of contigs is 36446. Cumulated length is 40.86Mb.
## Iran_2001_STIR01A18b
## Number of contigs is 36155. Cumulated length is 40.67Mb.
## Iran_2001_STIR01A28a
## Number of contigs is 36408. Cumulated length is 40.86Mb.
## Iran_2001_STIR01A32a
## Number of contigs is 42910. Cumulated length is 42.05Mb.
## Iran_2001_STIR01A37a
## Number of contigs is 27876. Cumulated length is 38.12Mb.
## Iran_2001_STIR01A44a
## Number of contigs is 28617. Cumulated length is 38.04Mb.
## Iran_2001_STIR01A48b
## Number of contigs is 46941. Cumulated length is 43.71Mb.
## Iran_2001_STIR01A78b
## Number of contigs is 24778. Cumulated length is 38.04Mb.
## Iran_2001_STIR01A97a
## Number of contigs is 28298. Cumulated length is 38.16Mb.
## Iran_2001_STIR01B74a
## Number of contigs is 49202. Cumulated length is 44.0Mb.
## Iran_2001_STIR01B74b
## Number of contigs is 48731. Cumulated length is 44.03Mb.
## Iran_2001_STIR01B76a
## Number of contigs is 55831. Cumulated length is 45.85Mb.
## Iran_2001_STIR01B78a
## Number of contigs is 53175. Cumulated length is 45.1Mb.
## Iran_2001_STIR01B83b
## Number of contigs is 32865. Cumulated length is 39.26Mb.
## Israel_1992_ISYB1b
## Number of contigs is 44796. Cumulated length is 42.12Mb.
## Israel_1992_ISYD3a_1
## Number of contigs is 37178. Cumulated length is 39.86Mb.
## Israel_1992_ISYH1a
## Number of contigs is 56345. Cumulated length is 43.12Mb.
## Israel_1992_ISZA1c
## Number of contigs is 45861. Cumulated length is 41.54Mb.
## Israel_1992_ISZB3a_1
## Number of contigs is 43677. Cumulated length is 41.94Mb.
## Israel_1992_ISZC1a
## Number of contigs is 40557. Cumulated length is 41.36Mb.
## Israel_1992_ISZC2a_2
## Number of contigs is 41568. Cumulated length is 41.29Mb.
## Israel_1992_ISZE1b_2
## Number of contigs is 38923. Cumulated length is 39.78Mb.
## Israel_1992_ISZF2a_1
## Number of contigs is 44886. Cumulated length is 40.98Mb.
## Israel_1992_ISZH2a
## Number of contigs is 43911. Cumulated length is 42.13Mb.
## Israel_1993_ISXBetC2a_1
## Number of contigs is 46233. Cumulated length is 42.63Mb.
## Israel_1993_ISXBetD4a_1
## Number of contigs is 43500. Cumulated length is 41.51Mb.
## Israel_1993_ISXBetH3a_4
## Number of contigs is 42052. Cumulated length is 41.01Mb.
## Kenya_1994_STKE94MF1a
## Number of contigs is 27025. Cumulated length is 39.21Mb.
## Kenya_1994_STKE94MI1a
## Number of contigs is 26559. Cumulated length is 39.25Mb.
## Kenya_1994_STKE94ML1a
## Number of contigs is 30206. Cumulated length is 40.53Mb.
## Missouri_1994_ST94MO12a_1
## Number of contigs is 33661. Cumulated length is 40.24Mb.
## Missouri_1994_ST94MO15a_1
## Number of contigs is 37798. Cumulated length is 40.89Mb.
## Missouri_1994_ST94MO17a_1
## Number of contigs is 100063. Cumulated length is 65.15Mb.
## Missouri_1994_ST94MO19a_1
## Number of contigs is 28945. Cumulated length is 40.14Mb.
## Missouri_1994_ST94MO24a_1
## Number of contigs is 71320. Cumulated length is 50.32Mb.
## Missouri_1994_ST94MO2a_1
## Number of contigs is 34961. Cumulated length is 40.51Mb.
## Missouri_1994_ST94MO33a_1
## Number of contigs is 80659. Cumulated length is 52.54Mb.
## Missouri_1994_ST94MO35a_1
## Number of contigs is 29858. Cumulated length is 39.86Mb.
## Missouri_1994_ST94MO8a_1
## Number of contigs is 69201. Cumulated length is 50.16Mb.
## Missouri_1994_ST94Mo31a_1
## Number of contigs is 29613. Cumulated length is 40.11Mb.
## NTC_1
## Number of contigs is 157. Cumulated length is 0.04Mb.
## NTC_2
## Number of contigs is 1667. Cumulated length is 0.51Mb.
## ST00ARG_BD0069
## Number of contigs is 117672. Cumulated length is 43.4Mb.
## ST00ARG_BD1D1a1
## Number of contigs is 118534. Cumulated length is 43.46Mb.
## ST01AUS_1A4
## Number of contigs is 75367. Cumulated length is 38.43Mb.
## ST01AUS_1A5
## Number of contigs is 103564. Cumulated length is 41.07Mb.
## ST01AUS_1A6
## Number of contigs is 95422. Cumulated length is 41.01Mb.
## ST01AUS_1A9
## Number of contigs is 94943. Cumulated length is 40.69Mb.
## ST01AUS_1B1
## Number of contigs is 53486. Cumulated length is 37.16Mb.
## ST01AUS_1B2
## Number of contigs is 100897. Cumulated length is 40.51Mb.
## ST01AUS_1B7
## Number of contigs is 121716. Cumulated length is 43.04Mb.
## ST01AUS_1B8
## Number of contigs is 99822. Cumulated length is 41.24Mb.
## ST01AUS_1C1
## Number of contigs is 73984. Cumulated length is 38.8Mb.
## ST01AUS_1C2
## Number of contigs is 77042. Cumulated length is 38.94Mb.
## ST01AUS_1C3
## Number of contigs is 97666. Cumulated length is 40.7Mb.
## ST01AUS_1C6
## Number of contigs is 68312. Cumulated length is 36.87Mb.
## ST01AUS_1C8
## Number of contigs is 130429. Cumulated length is 42.56Mb.
## ST01AUS_1D4
## Number of contigs is 96751. Cumulated length is 40.64Mb.
## ST01AUS_1D5
## Number of contigs is 94825. Cumulated length is 40.64Mb.
## ST01AUS_1D8
## Number of contigs is 100165. Cumulated length is 40.93Mb.
## ST01AUS_1E1
## Number of contigs is 81215. Cumulated length is 38.08Mb.
## ST01AUS_1E4
## Number of contigs is 71519. Cumulated length is 37.36Mb.
## ST01AUS_1E5
## Number of contigs is 103549. Cumulated length is 41.25Mb.
## ST01AUS_1F2
## Number of contigs is 88971. Cumulated length is 40.13Mb.
## ST01AUS_1F3
## Number of contigs is 85626. Cumulated length is 39.88Mb.
## ST01AUS_1F8
## Number of contigs is 69048. Cumulated length is 38.15Mb.
## ST01AUS_1G2
## Number of contigs is 70798. Cumulated length is 37.93Mb.
## ST01AUS_1G5
## Number of contigs is 104168. Cumulated length is 41.71Mb.
## ST01AUS_1H2
## Number of contigs is 94012. Cumulated length is 40.84Mb.
## ST01AUS_1H6
## Number of contigs is 116243. Cumulated length is 42.62Mb.
## ST01AUS_1H8
## Number of contigs is 71137. Cumulated length is 38.43Mb.
## ST05DK_01B5
## Number of contigs is 101313. Cumulated length is 42.5Mb.
## ST05DK_01a1
## Number of contigs is 116357. Cumulated length is 43.91Mb.
## ST05DK_01a4
## Number of contigs is 112627. Cumulated length is 42.95Mb.
## ST05DK_01ab1
## Number of contigs is 2073. Cumulated length is 32.84Mb.
## ST06FR_Biog_G84
## Number of contigs is 84144. Cumulated length is 41.82Mb.
## ST07SP_Biog_G85
## Number of contigs is 5245. Cumulated length is 33.87Mb.
## ST08TN_26_5_4
## Number of contigs is 114717. Cumulated length is 43.81Mb.
## ST09FR_Biog_G01
## Number of contigs is 276495. Cumulated length is 65.8Mb.
## ST09FR_Biog_G02
## Number of contigs is 60047. Cumulated length is 38.77Mb.
## ST09FR_Biog_G03
## Number of contigs is 84182. Cumulated length is 42.15Mb.
## ST09FR_Biog_G04
## Number of contigs is 73359. Cumulated length is 40.89Mb.
## ST09FR_Biog_G05
## Number of contigs is 69636. Cumulated length is 40.2Mb.
## ST09FR_Biog_G06
## Number of contigs is 73794. Cumulated length is 40.07Mb.
## ST09FR_Biog_G07
## Number of contigs is 70906. Cumulated length is 40.38Mb.
## ST09FR_Biog_G08
## Number of contigs is 103895. Cumulated length is 42.84Mb.
## ST09FR_Biog_G09
## Number of contigs is 79799. Cumulated length is 40.99Mb.
## ST09FR_Biog_G10
## Number of contigs is 74565. Cumulated length is 40.85Mb.
## ST09FR_Biog_G11
## Number of contigs is 94155. Cumulated length is 42.56Mb.
## ST09FR_Biog_G12
## Number of contigs is 75145. Cumulated length is 41.45Mb.
## ST09FR_Biog_G13
## Number of contigs is 84689. Cumulated length is 41.84Mb.
## ST09FR_Biog_G14
## Number of contigs is 84176. Cumulated length is 42.17Mb.
## ST09FR_Biog_G15
## Number of contigs is 96719. Cumulated length is 41.67Mb.
## ST09FR_Biog_G16
## Number of contigs is 74301. Cumulated length is 41.46Mb.
## ST09FR_Biog_G17
## Number of contigs is 70905. Cumulated length is 41.12Mb.
## ST09FR_Biog_G18
## Number of contigs is 96036. Cumulated length is 43.45Mb.
## ST09FR_Biog_G19
## Number of contigs is 98844. Cumulated length is 43.59Mb.
## ST09FR_Biog_G20
## Number of contigs is 73082. Cumulated length is 41.63Mb.
## ST09FR_Biog_G21
## Number of contigs is 85141. Cumulated length is 41.61Mb.
## ST09FR_Biog_G22
## Number of contigs is 63034. Cumulated length is 38.2Mb.
## ST09FR_Biog_G23
## Number of contigs is 52417. Cumulated length is 41.06Mb.
## ST09FR_Biog_G24
## Number of contigs is 70943. Cumulated length is 39.83Mb.
## ST09FR_Biog_G25
## Number of contigs is 70758. Cumulated length is 40.34Mb.
## ST09FR_Biog_G26
## Number of contigs is 66509. Cumulated length is 40.28Mb.
## ST09FR_Biog_G27
## Number of contigs is 68844. Cumulated length is 40.67Mb.
## ST09FR_Biog_G28
## Number of contigs is 78163. Cumulated length is 41.5Mb.
## ST09FR_Biog_G29
## Number of contigs is 77720. Cumulated length is 41.21Mb.
## ST09FR_Biog_G30
## Number of contigs is 78253. Cumulated length is 41.82Mb.
## ST09FR_Biog_G31
## Number of contigs is 73677. Cumulated length is 41.54Mb.
## ST09FR_Biog_G32
## Number of contigs is 58422. Cumulated length is 41.59Mb.
## ST09FR_Biog_G33
## Number of contigs is 69520. Cumulated length is 41.66Mb.
## ST09FR_Biog_G34
## Number of contigs is 61136. Cumulated length is 40.83Mb.
## ST09FR_Biog_G35
## Number of contigs is 88318. Cumulated length is 42.32Mb.
## ST09FR_Biog_G36
## Number of contigs is 70270. Cumulated length is 39.99Mb.
## ST09FR_Biog_G37
## Number of contigs is 83083. Cumulated length is 41.6Mb.
## ST09FR_Biog_G38
## Number of contigs is 66332. Cumulated length is 42.17Mb.
## ST09FR_Biog_G39
## Number of contigs is 54473. Cumulated length is 39.02Mb.
## ST09FR_Biog_G40
## Number of contigs is 63794. Cumulated length is 41.3Mb.
## ST09FR_Biog_G41
## Number of contigs is 78842. Cumulated length is 42.52Mb.
## ST09FR_Biog_G42
## Number of contigs is 56193. Cumulated length is 40.41Mb.
## ST09FR_Biog_G43
## Number of contigs is 61373. Cumulated length is 40.85Mb.
## ST09FR_Biog_G44
## Number of contigs is 67231. Cumulated length is 41.38Mb.
## ST09FR_Biog_G45
## Number of contigs is 65286. Cumulated length is 40.62Mb.
## ST09FR_Biog_G46
## Number of contigs is 70262. Cumulated length is 41.9Mb.
## ST09FR_Biog_G47
## Number of contigs is 50340. Cumulated length is 38.94Mb.
## ST09FR_Biog_G48
## Number of contigs is 72312. Cumulated length is 41.76Mb.
## ST09FR_Biog_G49
## Number of contigs is 64721. Cumulated length is 39.69Mb.
## ST09FR_Biog_G50
## Number of contigs is 54335. Cumulated length is 38.35Mb.
## ST09FR_Biog_G51
## Number of contigs is 92342. Cumulated length is 42.35Mb.
## ST09FR_Biog_G52
## Number of contigs is 55970. Cumulated length is 40.52Mb.
## ST09FR_Biog_G53
## Number of contigs is 74714. Cumulated length is 40.61Mb.
## ST09FR_Biog_G54
## Number of contigs is 54164. Cumulated length is 39.39Mb.
## ST09FR_Biog_G55
## Number of contigs is 86176. Cumulated length is 41.46Mb.
## ST09FR_Biog_G56
## Number of contigs is 72526. Cumulated length is 41.7Mb.
## ST09FR_Biog_G57
## Number of contigs is 61450. Cumulated length is 44.04Mb.
## ST09FR_Biog_G58
## Number of contigs is 55395. Cumulated length is 39.42Mb.
## ST09FR_Biog_G59
## Number of contigs is 67929. Cumulated length is 40.8Mb.
## ST09FR_Biog_G60
## Number of contigs is 70168. Cumulated length is 40.93Mb.
## ST09FR_Biog_G79
## Number of contigs is 89621. Cumulated length is 42.12Mb.
## ST09FR_Biog_G80
## Number of contigs is 79351. Cumulated length is 41.43Mb.
## ST09FR_Biog_G82
## Number of contigs is 70288. Cumulated length is 39.39Mb.
## ST09FR_Biog_I03
## Number of contigs is 60041. Cumulated length is 38.98Mb.
## ST09FR_Biog_I04
## Number of contigs is 77420. Cumulated length is 42.58Mb.
## ST09FR_Biog_I05
## Number of contigs is 80838. Cumulated length is 41.24Mb.
## ST09FR_Biog_I07
## Number of contigs is 76865. Cumulated length is 41.36Mb.
## ST09FR_Biog_I12
## Number of contigs is 93650. Cumulated length is 43.06Mb.
## ST09FR_Biog_I24
## Number of contigs is 84828. Cumulated length is 42.35Mb.
## ST09FR_Biog_I25
## Number of contigs is 88603. Cumulated length is 42.29Mb.
## ST09FR_Biog_I28
## Number of contigs is 70397. Cumulated length is 38.86Mb.
## ST10CRI_0450
## Number of contigs is 105974. Cumulated length is 42.47Mb.
## ST10CRI_0616
## Number of contigs is 112643. Cumulated length is 43.22Mb.
## ST10FR_Biog_G093
## Number of contigs is 82243. Cumulated length is 41.58Mb.
## ST10FR_Biog_G098
## Number of contigs is 95795. Cumulated length is 43.59Mb.
## ST10FR_Biog_G100
## Number of contigs is 76492. Cumulated length is 40.7Mb.
## ST10FR_Biog_G101
## Number of contigs is 77306. Cumulated length is 41.35Mb.
## ST10FR_Biog_G102
## Number of contigs is 89926. Cumulated length is 42.43Mb.
## ST10FR_Biog_G103
## Number of contigs is 82181. Cumulated length is 41.59Mb.
## ST10FR_Biog_G61
## Number of contigs is 56925. Cumulated length is 39.54Mb.
## ST10FR_Biog_G62
## Number of contigs is 77299. Cumulated length is 42.03Mb.
## ST10FR_Biog_G63
## Number of contigs is 75287. Cumulated length is 41.0Mb.
## ST10FR_Biog_G64
## Number of contigs is 80895. Cumulated length is 42.08Mb.
## ST10FR_Biog_G65
## Number of contigs is 75848. Cumulated length is 40.87Mb.
## ST10FR_Biog_G66
## Number of contigs is 66006. Cumulated length is 40.96Mb.
## ST10FR_Biog_G67
## Number of contigs is 70983. Cumulated length is 41.54Mb.
## ST10FR_Biog_G68
## Number of contigs is 68163. Cumulated length is 40.69Mb.
## ST10FR_Biog_G69
## Number of contigs is 65122. Cumulated length is 40.1Mb.
## ST10FR_Biog_G70
## Number of contigs is 59290. Cumulated length is 39.46Mb.
## ST10FR_Biog_G73
## Number of contigs is 86337. Cumulated length is 54.49Mb.
## ST10FR_Biog_G74
## Number of contigs is 58517. Cumulated length is 40.13Mb.
## ST10FR_Biog_G83
## Number of contigs is 75452. Cumulated length is 41.87Mb.
## ST10FR_Biog_G87
## Number of contigs is 86795. Cumulated length is 42.74Mb.
## ST10FR_Biog_G88
## Number of contigs is 86079. Cumulated length is 42.7Mb.
## ST10FR_Biog_G89
## Number of contigs is 76059. Cumulated length is 40.72Mb.
## ST10FR_Biog_G90
## Number of contigs is 77451. Cumulated length is 40.83Mb.
## ST10FR_Biog_G91
## Number of contigs is 72062. Cumulated length is 41.47Mb.
## ST10FR_Biog_G92
## Number of contigs is 67305. Cumulated length is 40.18Mb.
## ST10FR_Biog_G94
## Number of contigs is 81197. Cumulated length is 40.98Mb.
## ST10FR_Biog_G95
## Number of contigs is 86227. Cumulated length is 42.0Mb.
## ST10FR_Biog_G96
## Number of contigs is 80217. Cumulated length is 41.3Mb.
## ST10FR_Biog_G97
## Number of contigs is 76066. Cumulated length is 41.54Mb.
## ST10FR_Biog_G99
## Number of contigs is 105278. Cumulated length is 43.94Mb.
## ST13FR_Biog_LG0595
## Number of contigs is 86223. Cumulated length is 42.17Mb.
## ST13FR_Biog_SeptoDur10
## Number of contigs is 109299. Cumulated length is 43.89Mb.
## ST13FR_Biog_SeptoDur12
## Number of contigs is 105843. Cumulated length is 43.92Mb.
## ST13FR_Biog_SeptoDur29
## Number of contigs is 139312. Cumulated length is 45.66Mb.
## ST13FR_Biog_SeptoDur8
## Number of contigs is 91803. Cumulated length is 42.46Mb.
## ST13FR_Biog_SeptoDur82
## Number of contigs is 142631. Cumulated length is 46.54Mb.
## ST13FR_Biog_SeptoDur88
## Number of contigs is 114544. Cumulated length is 44.17Mb.
## ST13IT_Biog_1819
## Number of contigs is 114231. Cumulated length is 43.11Mb.
## ST13IT_Biog_1863
## Number of contigs is 208112. Cumulated length is 49.52Mb.
## ST13NZ_St13_4_1
## Number of contigs is 120442. Cumulated length is 44.69Mb.
## ST13NZ_St13_4_2
## Number of contigs is 118235. Cumulated length is 44.42Mb.
## ST13NZ_St13_4_3
## Number of contigs is 116289. Cumulated length is 44.33Mb.
## ST13NZ_St13_5_1
## Number of contigs is 128327. Cumulated length is 44.43Mb.
## ST13NZ_St13_5_2
## Number of contigs is 128020. Cumulated length is 45.29Mb.
## ST13NZ_St13_5_3
## Number of contigs is 120879. Cumulated length is 44.01Mb.
## ST13NZ_St13_5_4
## Number of contigs is 126452. Cumulated length is 44.52Mb.
## ST13NZ_St13_6_1
## Number of contigs is 122567. Cumulated length is 43.97Mb.
## ST13NZ_St13_6_2
## Number of contigs is 110767. Cumulated length is 43.22Mb.
## ST13NZ_St13_6_3
## Number of contigs is 112946. Cumulated length is 43.1Mb.
## ST13NZ_St13_6_4
## Number of contigs is 116333. Cumulated length is 43.47Mb.
## ST13NZ_St13_7_1
## Number of contigs is 113395. Cumulated length is 43.15Mb.
## ST13NZ_St13_7_2
## Number of contigs is 112497. Cumulated length is 43.52Mb.
## ST13NZ_St13_7_3
## Number of contigs is 117287. Cumulated length is 43.64Mb.
## ST13NZ_St13_7_4
## Number of contigs is 116671. Cumulated length is 43.61Mb.
## ST13NZ_St13_8_1
## Number of contigs is 112768. Cumulated length is 43.65Mb.
## ST13NZ_St13_8_2
## Number of contigs is 118313. Cumulated length is 44.06Mb.
## ST13NZ_St13_8_3
## Number of contigs is 130218. Cumulated length is 45.07Mb.
## ST13NZ_St13_8_4
## Number of contigs is 110103. Cumulated length is 42.95Mb.
## ST13NZ_St13_9_1
## Number of contigs is 119977. Cumulated length is 43.53Mb.
## ST13NZ_St13_9_2
## Number of contigs is 108569. Cumulated length is 42.62Mb.
## ST13NZ_St13_9_3
## Number of contigs is 110949. Cumulated length is 43.71Mb.
## ST13NZ_St13_9_4
## Number of contigs is 106959. Cumulated length is 42.86Mb.
## ST13SP_Biog_SeptoDur104
## Number of contigs is 114725. Cumulated length is 44.16Mb.
## ST14TAS_WAI1820
## Number of contigs is 150681. Cumulated length is 46.17Mb.
## ST14TAS_WAI1822
## Number of contigs is 158202. Cumulated length is 46.57Mb.
## ST14TAS_WAI1848
## Number of contigs is 147405. Cumulated length is 46.02Mb.
## ST14TAS_WAI1849
## Number of contigs is 134783. Cumulated length is 45.71Mb.
## ST14TAS_WAI1850
## Number of contigs is 119319. Cumulated length is 44.28Mb.
## ST14TAS_WAI1851
## Number of contigs is 146379. Cumulated length is 46.28Mb.
## ST14TAS_WAI1852
## Number of contigs is 119934. Cumulated length is 44.27Mb.
## ST14TAS_WAI1857
## Number of contigs is 20084. Cumulated length is 6.5Mb.
## ST14TAS_WAI1858
## Number of contigs is 132178. Cumulated length is 44.86Mb.
## ST14TAS_WAI1859
## Number of contigs is 138605. Cumulated length is 45.37Mb.
## ST14TAS_WAI1875
## Number of contigs is 128577. Cumulated length is 44.75Mb.
## ST14TAS_WAI1876
## Number of contigs is 124499. Cumulated length is 44.65Mb.
## ST14TAS_WAI1877
## Number of contigs is 175909. Cumulated length is 48.5Mb.
## ST14TAS_WAI1878
## Number of contigs is 146388. Cumulated length is 46.32Mb.
## ST14TAS_WAI1879
## Number of contigs is 113672. Cumulated length is 43.52Mb.
## ST14TAS_WAI1880
## Number of contigs is 150382. Cumulated length is 46.31Mb.
## ST14TAS_WAI1881
## Number of contigs is 25564. Cumulated length is 8.79Mb.
## ST14TAS_WAI1883
## Number of contigs is 23308. Cumulated length is 7.72Mb.
## ST14TAS_WAI1892
## Number of contigs is 137156. Cumulated length is 45.89Mb.
## ST14TAS_WAI1895
## Number of contigs is 135364. Cumulated length is 45.39Mb.
## ST14TAS_WAI1901
## Number of contigs is 140761. Cumulated length is 45.94Mb.
## ST14TAS_WAI1903
## Number of contigs is 144926. Cumulated length is 45.51Mb.
## ST14TAS_WAI1904
## Number of contigs is 142110. Cumulated length is 45.31Mb.
## ST14TAS_WAI1919
## Number of contigs is 115514. Cumulated length is 44.11Mb.
## ST14TAS_WAI1922
## Number of contigs is 161265. Cumulated length is 46.64Mb.
## ST14TAS_WAI1939
## Number of contigs is 146581. Cumulated length is 45.82Mb.
## ST14TAS_WAI1941
## Number of contigs is 104091. Cumulated length is 42.79Mb.
## ST14TAS_WAI1955
## Number of contigs is 109051. Cumulated length is 43.13Mb.
## ST14TAS_WAI1957
## Number of contigs is 125647. Cumulated length is 43.34Mb.
## ST14TAS_WAI1965
## Number of contigs is 315402. Cumulated length is 58.06Mb.
## ST14TAS_WAI1966
## Number of contigs is 153922. Cumulated length is 45.86Mb.
## ST14TAS_WAI1967
## Number of contigs is 137842. Cumulated length is 44.13Mb.
## ST14TAS_WAI1968
## Number of contigs is 147013. Cumulated length is 46.03Mb.
## ST14TAS_WAI1969
## Number of contigs is 138012. Cumulated length is 44.52Mb.
## ST14TAS_WAI1970
## Number of contigs is 144293. Cumulated length is 44.99Mb.
## ST14TAS_WAI1970D
## Number of contigs is 124584. Cumulated length is 43.53Mb.
## ST14TAS_WAI1971
## Number of contigs is 106504. Cumulated length is 56.19Mb.
## ST14TAS_WAI1972
## Number of contigs is 160351. Cumulated length is 46.48Mb.
## ST14TAS_WAI1993
## Number of contigs is 65063. Cumulated length is 42.7Mb.
## ST14TAS_WAI1998
## Number of contigs is 109754. Cumulated length is 48.67Mb.
## ST14TAS_WAI2000
## Number of contigs is 112807. Cumulated length is 43.87Mb.
## ST14TAS_WAI2029
## Number of contigs is 237790. Cumulated length is 55.62Mb.
## ST14TAS_WAI2031
## Number of contigs is 106668. Cumulated length is 42.98Mb.
## ST14TAS_WAI2045
## Number of contigs is 159642. Cumulated length is 47.02Mb.
## ST14TAS_WAI2047
## Number of contigs is 149096. Cumulated length is 46.58Mb.
## ST14TAS_WAI2059
## Number of contigs is 129178. Cumulated length is 44.41Mb.
## ST14TAS_WAI2060
## Number of contigs is 124247. Cumulated length is 44.71Mb.
## ST14TAS_WAI2061
## Number of contigs is 109264. Cumulated length is 43.1Mb.
## ST14TAS_WAI2073
## Number of contigs is 114337. Cumulated length is 43.65Mb.
## ST14TAS_WAI2077
## Number of contigs is 170576. Cumulated length is 48.29Mb.
## ST14TAS_WAI2203
## Number of contigs is 105913. Cumulated length is 42.79Mb.
## ST14TAS_WAI2204
## Number of contigs is 122304. Cumulated length is 44.28Mb.
## ST14TAS_WAI2206
## Number of contigs is 108766. Cumulated length is 42.85Mb.
## ST14TAS_WAI2208
## Number of contigs is 114596. Cumulated length is 43.99Mb.
## ST14TAS_WAI2210
## Number of contigs is 115470. Cumulated length is 42.78Mb.
## ST14TAS_WAI2216
## Number of contigs is 104217. Cumulated length is 42.89Mb.
## ST14TAS_WAI2226
## Number of contigs is 137384. Cumulated length is 45.3Mb.
## ST14TAS_WAI2228
## Number of contigs is 107531. Cumulated length is 42.94Mb.
## ST14TAS_WAI2230
## Number of contigs is 132394. Cumulated length is 44.85Mb.
## ST14TAS_WAI2232
## Number of contigs is 148424. Cumulated length is 46.39Mb.
## ST14UK_Biog_TMW07D8
## Number of contigs is 87567. Cumulated length is 40.92Mb.
## ST15NZ_St_15601_1
## Number of contigs is 106506. Cumulated length is 42.51Mb.
## ST15NZ_St_15601_10
## Number of contigs is 115348. Cumulated length is 43.1Mb.
## ST15NZ_St_15601_11
## Number of contigs is 110760. Cumulated length is 42.84Mb.
## ST15NZ_St_15601_12
## Number of contigs is 112790. Cumulated length is 42.97Mb.
## ST15NZ_St_15601_13
## Number of contigs is 118209. Cumulated length is 43.38Mb.
## ST15NZ_St_15601_14
## Number of contigs is 113493. Cumulated length is 43.02Mb.
## ST15NZ_St_15601_15
## Number of contigs is 111803. Cumulated length is 42.87Mb.
## ST15NZ_St_15601_16
## Number of contigs is 114714. Cumulated length is 43.13Mb.
## ST15NZ_St_15601_17
## Number of contigs is 113643. Cumulated length is 43.04Mb.
## ST15NZ_St_15601_18
## Number of contigs is 114034. Cumulated length is 43.07Mb.
## ST15NZ_St_15601_19
## Number of contigs is 118526. Cumulated length is 43.36Mb.
## ST15NZ_St_15601_2
## Number of contigs is 115006. Cumulated length is 43.13Mb.
## ST15NZ_St_15601_20
## Number of contigs is 116692. Cumulated length is 43.85Mb.
## ST15NZ_St_15601_3
## Number of contigs is 115931. Cumulated length is 43.21Mb.
## ST15NZ_St_15601_4
## Number of contigs is 114240. Cumulated length is 43.09Mb.
## ST15NZ_St_15601_5
## Number of contigs is 130740. Cumulated length is 45.01Mb.
## ST15NZ_St_15601_6
## Number of contigs is 111791. Cumulated length is 42.91Mb.
## ST15NZ_St_15601_7
## Number of contigs is 116605. Cumulated length is 43.24Mb.
## ST15NZ_St_15601_8
## Number of contigs is 115557. Cumulated length is 43.12Mb.
## ST15NZ_St_15601_9
## Number of contigs is 133794. Cumulated length is 45.21Mb.
## ST15NZ_St_15640_1
## Number of contigs is 113194. Cumulated length is 43.26Mb.
## ST15NZ_St_15640_10
## Number of contigs is 124441. Cumulated length is 44.74Mb.
## ST15NZ_St_15640_11
## Number of contigs is 108188. Cumulated length is 42.83Mb.
## ST15NZ_St_15640_12
## Number of contigs is 124151. Cumulated length is 44.72Mb.
## ST15NZ_St_15640_2
## Number of contigs is 114501. Cumulated length is 43.95Mb.
## ST15NZ_St_15640_3
## Number of contigs is 114464. Cumulated length is 43.68Mb.
## ST15NZ_St_15640_4
## Number of contigs is 118364. Cumulated length is 43.95Mb.
## ST15NZ_St_15640_5
## Number of contigs is 123476. Cumulated length is 44.68Mb.
## ST15NZ_St_15640_6
## Number of contigs is 122718. Cumulated length is 44.62Mb.
## ST15NZ_St_15640_7
## Number of contigs is 148849. Cumulated length is 47.74Mb.
## ST15NZ_St_15640_8
## Number of contigs is 113844. Cumulated length is 43.61Mb.
## ST15NZ_St_15640_9
## Number of contigs is 127736. Cumulated length is 44.38Mb.
## ST15NZ_St_15642_1
## Number of contigs is 131105. Cumulated length is 44.45Mb.
## ST15NZ_St_15642_10
## Number of contigs is 103343. Cumulated length is 41.71Mb.
## ST15NZ_St_15642_11
## Number of contigs is 107688. Cumulated length is 41.76Mb.
## ST15NZ_St_15642_12
## Number of contigs is 103814. Cumulated length is 42.21Mb.
## ST15NZ_St_15642_13
## Number of contigs is 110881. Cumulated length is 42.86Mb.
## ST15NZ_St_15642_14
## Number of contigs is 115580. Cumulated length is 46.99Mb.
## ST15NZ_St_15642_15
## Number of contigs is 135846. Cumulated length is 44.93Mb.
## ST15NZ_St_15642_16
## Number of contigs is 108071. Cumulated length is 42.24Mb.
## ST15NZ_St_15642_17
## Number of contigs is 121106. Cumulated length is 43.79Mb.
## ST15NZ_St_15642_18
## Number of contigs is 129295. Cumulated length is 44.68Mb.
## ST15NZ_St_15642_19
## Number of contigs is 121448. Cumulated length is 49.42Mb.
## ST15NZ_St_15642_2
## Number of contigs is 141910. Cumulated length is 45.96Mb.
## ST15NZ_St_15642_20
## Number of contigs is 118866. Cumulated length is 42.84Mb.
## ST15NZ_St_15642_21
## Number of contigs is 125458. Cumulated length is 44.04Mb.
## ST15NZ_St_15642_22
## Number of contigs is 111212. Cumulated length is 43.08Mb.
## ST15NZ_St_15642_23
## Number of contigs is 137815. Cumulated length is 45.19Mb.
## ST15NZ_St_15642_3
## Number of contigs is 121471. Cumulated length is 43.5Mb.
## ST15NZ_St_15642_4
## Number of contigs is 123416. Cumulated length is 45.44Mb.
## ST15NZ_St_15642_8
## Number of contigs is 164543. Cumulated length is 47.55Mb.
## ST15NZ_St_15642_9
## Number of contigs is 123982. Cumulated length is 44.32Mb.
## ST15ORE_Mad_A1
## Number of contigs is 60392. Cumulated length is 43.45Mb.
## ST15ORE_Mad_A2
## Number of contigs is 57846. Cumulated length is 42.59Mb.
## ST15ORE_Mad_A3
## Number of contigs is 60616. Cumulated length is 43.44Mb.
## ST15ORE_Mad_A4
## Number of contigs is 58841. Cumulated length is 43.29Mb.
## ST15ORE_Mad_A5
## Number of contigs is 64518. Cumulated length is 44.34Mb.
## ST15ORE_Mad_A6
## Number of contigs is 58147. Cumulated length is 42.76Mb.
## ST15ORE_Mad_A7
## Number of contigs is 63644. Cumulated length is 43.83Mb.
## ST15ORE_Mad_B1
## Number of contigs is 62916. Cumulated length is 43.3Mb.
## ST15ORE_Mad_B3
## Number of contigs is 64936. Cumulated length is 43.37Mb.
## ST15ORE_Mad_B4
## Number of contigs is 52511. Cumulated length is 41.24Mb.
## ST15ORE_Mad_B5
## Number of contigs is 56665. Cumulated length is 42.74Mb.
## ST15ORE_Mad_C1
## Number of contigs is 59667. Cumulated length is 43.2Mb.
## ST15ORE_Mad_C2
## Number of contigs is 57704. Cumulated length is 42.27Mb.
## ST15ORE_Mad_C3
## Number of contigs is 73246. Cumulated length is 45.35Mb.
## ST15ORE_Mad_C4
## Number of contigs is 55931. Cumulated length is 41.76Mb.
## ST15ORE_Mad_C5
## Number of contigs is 62055. Cumulated length is 43.83Mb.
## ST15ORE_Mad_C6
## Number of contigs is 62560. Cumulated length is 43.27Mb.
## ST15ORE_Mad_C7
## Number of contigs is 58136. Cumulated length is 42.31Mb.
## ST15ORE_Mad_D1
## Number of contigs is 63139. Cumulated length is 43.81Mb.
## ST15ORE_Mad_D2
## Number of contigs is 59981. Cumulated length is 42.74Mb.
## ST15ORE_Mad_D3
## Number of contigs is 65644. Cumulated length is 44.01Mb.
## ST15ORE_Mad_D4
## Number of contigs is 68144. Cumulated length is 44.49Mb.
## ST15ORE_Mad_D5
## Number of contigs is 62684. Cumulated length is 43.24Mb.
## ST15ORE_Mad_D6
## Number of contigs is 58071. Cumulated length is 42.39Mb.
## ST15ORE_Mad_E1
## Number of contigs is 60284. Cumulated length is 43.16Mb.
## ST15ORE_Mad_E2
## Number of contigs is 59733. Cumulated length is 42.6Mb.
## ST15ORE_Mad_E3
## Number of contigs is 63618. Cumulated length is 42.98Mb.
## ST15ORE_Mad_E4
## Number of contigs is 55917. Cumulated length is 41.89Mb.
## ST15ORE_Mad_E5
## Number of contigs is 60487. Cumulated length is 43.33Mb.
## ST15ORE_Mad_E6
## Number of contigs is 58716. Cumulated length is 43.05Mb.
## ST15ORE_Mad_E7
## Number of contigs is 59068. Cumulated length is 43.84Mb.
## ST15ORE_Mad_F1
## Number of contigs is 64975. Cumulated length is 43.72Mb.
## ST15ORE_Mad_F2
## Number of contigs is 60558. Cumulated length is 42.3Mb.
## ST15ORE_Mad_F3
## Number of contigs is 46503. Cumulated length is 41.51Mb.
## ST15ORE_Mad_F4
## Number of contigs is 62260. Cumulated length is 43.31Mb.
## ST15ORE_Mad_F5
## Number of contigs is 51071. Cumulated length is 39.73Mb.
## ST15ORE_Mad_F6
## Number of contigs is 56433. Cumulated length is 42.77Mb.
## ST15ORE_Mad_G1
## Number of contigs is 65119. Cumulated length is 44.07Mb.
## ST15ORE_Mad_G2
## Number of contigs is 62446. Cumulated length is 43.44Mb.
## ST15ORE_Mad_G3
## Number of contigs is 59330. Cumulated length is 42.45Mb.
## ST15ORE_Mad_G4
## Number of contigs is 58094. Cumulated length is 42.35Mb.
## ST15ORE_Mad_G5
## Number of contigs is 65079. Cumulated length is 44.17Mb.
## ST15ORE_Mad_H1
## Number of contigs is 66442. Cumulated length is 44.4Mb.
## ST15ORE_Mad_H2
## Number of contigs is 61328. Cumulated length is 42.58Mb.
## ST15ORE_Mad_H3
## Number of contigs is 67223. Cumulated length is 44.09Mb.
## ST15ORE_Mad_H4
## Number of contigs is 57389. Cumulated length is 42.96Mb.
## ST15ORE_Mad_H7
## Number of contigs is 61665. Cumulated length is 43.83Mb.
## ST15ORE_Ste_A1
## Number of contigs is 65434. Cumulated length is 44.06Mb.
## ST15ORE_Ste_A10
## Number of contigs is 60160. Cumulated length is 42.06Mb.
## ST15ORE_Ste_A11
## Number of contigs is 62720. Cumulated length is 43.78Mb.
## ST15ORE_Ste_A12
## Number of contigs is 62343. Cumulated length is 43.09Mb.
## ST15ORE_Ste_A13
## Number of contigs is 55976. Cumulated length is 42.33Mb.
## ST15ORE_Ste_A14
## Number of contigs is 64357. Cumulated length is 43.79Mb.
## ST15ORE_Ste_A15
## Number of contigs is 68753. Cumulated length is 44.1Mb.
## ST15ORE_Ste_A16
## Number of contigs is 61489. Cumulated length is 42.97Mb.
## ST15ORE_Ste_A17
## Number of contigs is 63882. Cumulated length is 43.13Mb.
## ST15ORE_Ste_A18
## Number of contigs is 57814. Cumulated length is 42.93Mb.
## ST15ORE_Ste_A19
## Number of contigs is 58097. Cumulated length is 43.37Mb.
## ST15ORE_Ste_A2
## Number of contigs is 54637. Cumulated length is 42.59Mb.
## ST15ORE_Ste_A20
## Number of contigs is 56590. Cumulated length is 42.58Mb.
## ST15ORE_Ste_A21
## Number of contigs is 60023. Cumulated length is 43.28Mb.
## ST15ORE_Ste_A22
## Number of contigs is 60288. Cumulated length is 43.02Mb.
## ST15ORE_Ste_A23
## Number of contigs is 61487. Cumulated length is 43.65Mb.
## ST15ORE_Ste_A24
## Number of contigs is 62590. Cumulated length is 43.36Mb.
## ST15ORE_Ste_A25
## Number of contigs is 62013. Cumulated length is 43.83Mb.
## ST15ORE_Ste_A26
## Number of contigs is 68334. Cumulated length is 44.15Mb.
## ST15ORE_Ste_A27
## Number of contigs is 61354. Cumulated length is 43.69Mb.
## ST15ORE_Ste_A3
## Number of contigs is 57297. Cumulated length is 42.53Mb.
## ST15ORE_Ste_A4
## Number of contigs is 58416. Cumulated length is 43.09Mb.
## ST15ORE_Ste_A5
## Number of contigs is 53416. Cumulated length is 42.44Mb.
## ST15ORE_Ste_A6
## Number of contigs is 62829. Cumulated length is 43.57Mb.
## ST15ORE_Ste_A7
## Number of contigs is 63239. Cumulated length is 44.15Mb.
## ST15ORE_Ste_A8
## Number of contigs is 62576. Cumulated length is 42.9Mb.
## ST15ORE_Ste_A9
## Number of contigs is 62346. Cumulated length is 43.51Mb.
## ST15ORE_Ste_B1
## Number of contigs is 63880. Cumulated length is 43.71Mb.
## ST15ORE_Ste_B10
## Number of contigs is 56470. Cumulated length is 43.07Mb.
## ST15ORE_Ste_B11
## Number of contigs is 62432. Cumulated length is 43.04Mb.
## ST15ORE_Ste_B12
## Number of contigs is 61304. Cumulated length is 43.5Mb.
## ST15ORE_Ste_B14
## Number of contigs is 60082. Cumulated length is 43.05Mb.
## ST15ORE_Ste_B15
## Number of contigs is 58632. Cumulated length is 42.68Mb.
## ST15ORE_Ste_B16
## Number of contigs is 58261. Cumulated length is 42.41Mb.
## ST15ORE_Ste_B17
## Number of contigs is 54731. Cumulated length is 42.28Mb.
## ST15ORE_Ste_B18
## Number of contigs is 64459. Cumulated length is 43.71Mb.
## ST15ORE_Ste_B19
## Number of contigs is 61731. Cumulated length is 43.74Mb.
## ST15ORE_Ste_B2
## Number of contigs is 66569. Cumulated length is 43.89Mb.
## ST15ORE_Ste_B20
## Number of contigs is 58351. Cumulated length is 41.9Mb.
## ST15ORE_Ste_B21
## Number of contigs is 62917. Cumulated length is 43.41Mb.
## ST15ORE_Ste_B22
## Number of contigs is 59747. Cumulated length is 43.04Mb.
## ST15ORE_Ste_B23
## Number of contigs is 58628. Cumulated length is 43.01Mb.
## ST15ORE_Ste_B24
## Number of contigs is 64064. Cumulated length is 43.67Mb.
## ST15ORE_Ste_B3
## Number of contigs is 65926. Cumulated length is 44.27Mb.
## ST15ORE_Ste_B4
## Number of contigs is 66830. Cumulated length is 43.99Mb.
## ST15ORE_Ste_B5
## Number of contigs is 54996. Cumulated length is 42.53Mb.
## ST15ORE_Ste_B6
## Number of contigs is 61941. Cumulated length is 43.96Mb.
## ST15ORE_Ste_B7
## Number of contigs is 59845. Cumulated length is 42.97Mb.
## ST15ORE_Ste_B8
## Number of contigs is 63510. Cumulated length is 42.93Mb.
## ST15ORE_Ste_B9
## Number of contigs is 63660. Cumulated length is 44.15Mb.
## ST16ALG_Biog_Alg74
## Number of contigs is 159797. Cumulated length is 46.52Mb.
## ST16CH_1A1
## Number of contigs is 113452. Cumulated length is 42.37Mb.
## ST16CH_1A11
## Number of contigs is 102537. Cumulated length is 42.24Mb.
## ST16CH_1A27
## Number of contigs is 112820. Cumulated length is 43.51Mb.
## ST16CH_1A57
## Number of contigs is 109503. Cumulated length is 42.27Mb.
## ST16CH_1B31
## Number of contigs is 98148. Cumulated length is 42.86Mb.
## ST16CH_1B73
## Number of contigs is 105061. Cumulated length is 42.55Mb.
## ST16CH_1B8
## Number of contigs is 100888. Cumulated length is 42.86Mb.
## ST16CH_1C12
## Number of contigs is 106460. Cumulated length is 43.08Mb.
## ST16CH_1C31
## Number of contigs is 116534. Cumulated length is 43.65Mb.
## ST16CH_1C52
## Number of contigs is 101318. Cumulated length is 43.05Mb.
## ST16CH_1C65
## Number of contigs is 107325. Cumulated length is 42.14Mb.
## ST16CH_1D1
## Number of contigs is 88267. Cumulated length is 41.01Mb.
## ST16CH_1D15
## Number of contigs is 129154. Cumulated length is 43.21Mb.
## ST16CH_1D15_2
## Number of contigs is 89002. Cumulated length is 40.85Mb.
## ST16CH_1D23
## Number of contigs is 7833. Cumulated length is 35.93Mb.
## ST16CH_1D8
## Number of contigs is 87672. Cumulated length is 40.82Mb.
## ST16CH_1D8_2
## Number of contigs is 2328. Cumulated length is 33.0Mb.
## ST16CH_1E21
## Number of contigs is 91476. Cumulated length is 41.36Mb.
## ST16CH_1E43
## Number of contigs is 104092. Cumulated length is 42.68Mb.
## ST16CH_1E52
## Number of contigs is 103516. Cumulated length is 43.29Mb.
## ST16CH_1E52_2
## Number of contigs is 109284. Cumulated length is 43.21Mb.
## ST16CH_1E70
## Number of contigs is 28250. Cumulated length is 23.47Mb.
## ST16CH_1F1
## Number of contigs is 101012. Cumulated length is 41.08Mb.
## ST16CH_1F11
## Number of contigs is 106776. Cumulated length is 44.15Mb.
## ST16CH_1F19
## Number of contigs is 97446. Cumulated length is 41.16Mb.
## ST16CH_1F4
## Number of contigs is 161436. Cumulated length is 45.97Mb.
## ST16CH_1G30
## Number of contigs is 81425. Cumulated length is 38.37Mb.
## ST16CH_1G47
## Number of contigs is 104667. Cumulated length is 41.97Mb.
## ST16CH_1G8
## Number of contigs is 100491. Cumulated length is 41.68Mb.
## ST16CH_1H12
## Number of contigs is 74699. Cumulated length is 37.93Mb.
## ST16CH_1H32
## Number of contigs is 87015. Cumulated length is 41.58Mb.
## ST16CH_1H34
## Number of contigs is 109128. Cumulated length is 43.44Mb.
## ST16CH_1I10
## Number of contigs is 109912. Cumulated length is 42.87Mb.
## ST16CH_1I19
## Number of contigs is 1987. Cumulated length is 13.07Mb.
## ST16CH_1I3
## Number of contigs is 96111. Cumulated length is 41.71Mb.
## ST16CH_1K16
## Number of contigs is 123021. Cumulated length is 43.56Mb.
## ST16CH_1K29
## Number of contigs is 90138. Cumulated length is 41.13Mb.
## ST16CH_1K37
## Number of contigs is 2036. Cumulated length is 13.06Mb.
## ST16CH_1K42
## Number of contigs is 97422. Cumulated length is 42.94Mb.
## ST16CH_1L32
## Number of contigs is 111415. Cumulated length is 43.87Mb.
## ST16CH_1L40
## Number of contigs is 6303. Cumulated length is 1.98Mb.
## ST16CH_1L42
## Number of contigs is 30386. Cumulated length is 23.87Mb.
## ST16CH_1L46
## Number of contigs is 187492. Cumulated length is 48.43Mb.
## ST16CH_1M21
## Number of contigs is 103096. Cumulated length is 41.6Mb.
## ST16CH_1M28
## Number of contigs is 102044. Cumulated length is 42.94Mb.
## ST16CH_1M33
## Number of contigs is 112545. Cumulated length is 43.52Mb.
## ST16CH_1M59
## Number of contigs is 99596. Cumulated length is 41.72Mb.
## ST16CH_1N1
## Number of contigs is 103314. Cumulated length is 42.94Mb.
## ST16CH_1N25
## Number of contigs is 110649. Cumulated length is 43.51Mb.
## ST16CH_1N6
## Number of contigs is 104606. Cumulated length is 41.05Mb.
## ST16CH_1O25
## Number of contigs is 99180. Cumulated length is 43.11Mb.
## ST16CH_1O3
## Number of contigs is 92966. Cumulated length is 41.19Mb.
## ST16CH_1O40
## Number of contigs is 105133. Cumulated length is 42.21Mb.
## ST16CH_1O65
## Number of contigs is 90337. Cumulated length is 40.22Mb.
## ST16CH_1P22
## Number of contigs is 124431. Cumulated length is 43.71Mb.
## ST16CH_1P35
## Number of contigs is 117619. Cumulated length is 43.48Mb.
## ST16CH_1P56
## Number of contigs is 97. Cumulated length is 0.05Mb.
## ST16CH_1P56_2
## Number of contigs is 110974. Cumulated length is 42.78Mb.
## ST16CH_1P7
## Number of contigs is 54. Cumulated length is 0.02Mb.
## ST16CH_1P7_2
## Number of contigs is 104527. Cumulated length is 41.98Mb.
## ST16CH_1Q10
## Number of contigs is 85272. Cumulated length is 40.6Mb.
## ST16CH_1Q24
## Number of contigs is 124595. Cumulated length is 42.56Mb.
## ST16CH_1Q48
## Number of contigs is 116252. Cumulated length is 44.14Mb.
## ST16CH_1R15
## Number of contigs is 92. Cumulated length is 0.05Mb.
## ST16CH_1R15_2
## Number of contigs is 12076. Cumulated length is 30.61Mb.
## ST16CH_1R24
## Number of contigs is 110557. Cumulated length is 42.97Mb.
## ST16CH_1R36
## Number of contigs is 130113. Cumulated length is 44.66Mb.
## ST16CH_1R5
## Number of contigs is 104303. Cumulated length is 42.76Mb.
## ST16CH_1S10
## Number of contigs is 94291. Cumulated length is 41.49Mb.
## ST16CH_1S33
## Number of contigs is 98574. Cumulated length is 41.8Mb.
## ST16CH_1S7
## Number of contigs is 112219. Cumulated length is 42.98Mb.
## ST16CH_1S9
## Number of contigs is 103681. Cumulated length is 41.99Mb.
## ST16CH_1T2
## Number of contigs is 107746. Cumulated length is 43.01Mb.
## ST16CH_1T25
## Number of contigs is 109556. Cumulated length is 42.65Mb.
## ST16CH_1T52
## Number of contigs is 98814. Cumulated length is 41.7Mb.
## ST16CH_1U1
## Number of contigs is 122022. Cumulated length is 43.92Mb.
## ST16CH_1U30
## Number of contigs is 114122. Cumulated length is 43.78Mb.
## ST16CH_1U6
## Number of contigs is 100317. Cumulated length is 41.68Mb.
## ST16CH_1U9
## Number of contigs is 108889. Cumulated length is 43.02Mb.
## ST16CH_1V12
## Number of contigs is 99838. Cumulated length is 40.85Mb.
## ST16CH_1V20
## Number of contigs is 97362. Cumulated length is 41.84Mb.
## ST16CH_1V4
## Number of contigs is 223504. Cumulated length is 49.92Mb.
## ST16CH_1V50
## Number of contigs is 130552. Cumulated length is 44.51Mb.
## ST16CH_1W18
## Number of contigs is 91848. Cumulated length is 41.59Mb.
## ST16CH_1W32
## Number of contigs is 133819. Cumulated length is 44.92Mb.
## ST16CH_1W9
## Number of contigs is 117116. Cumulated length is 44.17Mb.
## ST16CH_1X1
## Number of contigs is 113694. Cumulated length is 42.65Mb.
## ST16CH_1X14
## Number of contigs is 105859. Cumulated length is 42.14Mb.
## ST16CH_1X23
## Number of contigs is 94369. Cumulated length is 41.98Mb.
## ST16CH_1X7
## Number of contigs is 95992. Cumulated length is 41.56Mb.
## ST16CH_2C1
## Number of contigs is 110643. Cumulated length is 42.47Mb.
## ST16CH_2C2
## Number of contigs is 96720. Cumulated length is 41.57Mb.
## ST16CH_2C5
## Number of contigs is 108223. Cumulated length is 42.83Mb.
## ST16CH_2C7
## Number of contigs is 87536. Cumulated length is 41.47Mb.
## ST16CH_2G10
## Number of contigs is 110219. Cumulated length is 40.97Mb.
## ST16CH_2G18
## Number of contigs is 97088. Cumulated length is 41.77Mb.
## ST16CH_2G34
## Number of contigs is 100815. Cumulated length is 42.71Mb.
## ST16CH_2G4
## Number of contigs is 99334. Cumulated length is 41.32Mb.
## ST16CH_2N5
## Number of contigs is 106978. Cumulated length is 42.69Mb.
## ST16CH_2O1
## Number of contigs is 92704. Cumulated length is 41.17Mb.
## ST16CH_2O4
## Number of contigs is 110721. Cumulated length is 43.51Mb.
## ST16CH_2O5
## Number of contigs is 4935. Cumulated length is 33.16Mb.
## ST16CH_2P1
## Number of contigs is 2325. Cumulated length is 33.78Mb.
## ST16CH_2P3
## Number of contigs is 109517. Cumulated length is 42.92Mb.
## ST16CH_2P5
## Number of contigs is 119570. Cumulated length is 43.65Mb.
## ST16CH_2P7
## Number of contigs is 120204. Cumulated length is 43.88Mb.
## ST16CH_2U14
## Number of contigs is 49. Cumulated length is 0.01Mb.
## ST16CH_2U14_2
## Number of contigs is 106025. Cumulated length is 42.91Mb.
## ST16CH_2U2
## Number of contigs is 140268. Cumulated length is 44.68Mb.
## ST16CH_2U24
## Number of contigs is 104920. Cumulated length is 42.98Mb.
## ST16CH_2U7
## Number of contigs is 96470. Cumulated length is 41.59Mb.
## ST16CH_2X10
## Number of contigs is 31531. Cumulated length is 26.4Mb.
## ST16CH_2X1xx
## Number of contigs is 104991. Cumulated length is 43.21Mb.
## ST16CH_2X2
## Number of contigs is 110753. Cumulated length is 43.32Mb.
## ST16CH_2Z1
## Number of contigs is 96957. Cumulated length is 41.01Mb.
## ST16CH_2gamma1
## Number of contigs is 129556. Cumulated length is 43.52Mb.
## ST16CH_3A16
## Number of contigs is 83175. Cumulated length is 40.69Mb.
## ST16CH_3A31
## Number of contigs is 100768. Cumulated length is 42.07Mb.
## ST16CH_3A36
## Number of contigs is 108072. Cumulated length is 42.51Mb.
## ST16CH_3A51
## Number of contigs is 93153. Cumulated length is 41.48Mb.
## ST16CH_3B1
## Number of contigs is 106234. Cumulated length is 42.98Mb.
## ST16CH_3B19
## Number of contigs is 7099. Cumulated length is 29.3Mb.
## ST16CH_3B36
## Number of contigs is 90864. Cumulated length is 41.34Mb.
## ST16CH_3B8
## Number of contigs is 91899. Cumulated length is 41.8Mb.
## ST16CH_3C19
## Number of contigs is 103690. Cumulated length is 42.63Mb.
## ST16CH_3C23
## Number of contigs is 93649. Cumulated length is 40.65Mb.
## ST16CH_3C6
## Number of contigs is 85720. Cumulated length is 40.47Mb.
## ST16CH_3C81
## Number of contigs is 84896. Cumulated length is 39.69Mb.
## ST16CH_3D1
## Number of contigs is 112603. Cumulated length is 43.65Mb.
## ST16CH_3D10
## Number of contigs is 104338. Cumulated length is 42.9Mb.
## ST16CH_3D6
## Number of contigs is 145934. Cumulated length is 45.28Mb.
## ST16CH_3D7
## Number of contigs is 91392. Cumulated length is 41.33Mb.
## ST16CH_3E23
## Number of contigs is 99075. Cumulated length is 42.15Mb.
## ST16CH_3E34
## Number of contigs is 154614. Cumulated length is 46.05Mb.
## ST16CH_3E45
## Number of contigs is 86338. Cumulated length is 41.37Mb.
## ST16CH_3E9
## Number of contigs is 102700. Cumulated length is 42.81Mb.
## ST16CH_3F2
## Number of contigs is 120400. Cumulated length is 44.79Mb.
## ST16CH_3F4
## Number of contigs is 98268. Cumulated length is 41.94Mb.
## ST16CH_3F7
## Number of contigs is 104178. Cumulated length is 42.87Mb.
## ST16CH_3F9
## Number of contigs is 104140. Cumulated length is 42.41Mb.
## ST16CH_3G26
## Number of contigs is 101553. Cumulated length is 41.53Mb.
## ST16CH_3G34
## Number of contigs is 37316. Cumulated length is 33.83Mb.
## ST16CH_3G46
## Number of contigs is 106510. Cumulated length is 42.73Mb.
## ST16CH_3G6
## Number of contigs is 91881. Cumulated length is 41.15Mb.
## ST16CH_3H26
## Number of contigs is 86554. Cumulated length is 40.08Mb.
## ST16CH_3H33
## Number of contigs is 70785. Cumulated length is 37.87Mb.
## ST16CH_3H33_2
## Number of contigs is 267233. Cumulated length is 62.12Mb.
## ST16CH_3H43
## Number of contigs is 212755. Cumulated length is 55.6Mb.
## ST16CH_3H49
## Number of contigs is 94970. Cumulated length is 41.61Mb.
## ST16CH_3I14
## Number of contigs is 101256. Cumulated length is 39.98Mb.
## ST16CH_3I23
## Number of contigs is 111111. Cumulated length is 43.0Mb.
## ST16CH_3I23_2
## Number of contigs is 97160. Cumulated length is 42.18Mb.
## ST16CH_3I5
## Number of contigs is 83008. Cumulated length is 39.97Mb.
## ST16CH_3I5_2
## Number of contigs is 19. Cumulated length is 0.0Mb.
## ST16CH_3K1
## Number of contigs is 87711. Cumulated length is 40.63Mb.
## ST16CH_3K32
## Number of contigs is 99377. Cumulated length is 42.77Mb.
## ST16CH_3K8
## Number of contigs is 3241. Cumulated length is 36.02Mb.
## ST16CH_3L2
## Number of contigs is 100932. Cumulated length is 42.13Mb.
## ST16CH_3L27
## Number of contigs is 4148. Cumulated length is 33.69Mb.
## ST16CH_3M19
## Number of contigs is 98557. Cumulated length is 41.48Mb.
## ST16CH_3M24
## Number of contigs is 116431. Cumulated length is 42.68Mb.
## ST16CH_3M3
## Number of contigs is 105007. Cumulated length is 43.65Mb.
## ST16CH_3M36
## Number of contigs is 104362. Cumulated length is 42.72Mb.
## ST16CH_3N27
## Number of contigs is 100805. Cumulated length is 42.53Mb.
## ST16CH_3N35
## Number of contigs is 114657. Cumulated length is 43.56Mb.
## ST16CH_3N48
## Number of contigs is 111241. Cumulated length is 42.22Mb.
## ST16CH_3N8
## Number of contigs is 116677. Cumulated length is 43.52Mb.
## ST16CH_3O21
## Number of contigs is 103911. Cumulated length is 43.48Mb.
## ST16CH_3O24
## Number of contigs is 96577. Cumulated length is 41.4Mb.
## ST16CH_3O9
## Number of contigs is 114500. Cumulated length is 43.08Mb.
## ST16CH_3P15
## Number of contigs is 107816. Cumulated length is 43.41Mb.
## ST16CH_3P2
## Number of contigs is 94848. Cumulated length is 41.52Mb.
## ST16CH_3P39
## Number of contigs is 110091. Cumulated length is 43.36Mb.
## ST16CH_3Q24
## Number of contigs is 95845. Cumulated length is 42.1Mb.
## ST16CH_3Q36
## Number of contigs is 104182. Cumulated length is 43.32Mb.
## ST16CH_3Q9
## Number of contigs is 107333. Cumulated length is 42.75Mb.
## ST16CH_3R1
## Number of contigs is 120135. Cumulated length is 44.37Mb.
## ST16CH_3R26
## Number of contigs is 108585. Cumulated length is 43.6Mb.
## ST16CH_3R32
## Number of contigs is 115003. Cumulated length is 44.11Mb.
## ST16CH_3R39
## Number of contigs is 114585. Cumulated length is 44.08Mb.
## ST16CH_3S1
## Number of contigs is 108502. Cumulated length is 43.34Mb.
## ST16CH_3S9
## Number of contigs is 102390. Cumulated length is 41.73Mb.
## ST16CH_3T31
## Number of contigs is 110426. Cumulated length is 43.24Mb.
## ST16CH_3T39
## Number of contigs is 106871. Cumulated length is 42.31Mb.
## ST16CH_3T5
## Number of contigs is 109809. Cumulated length is 43.28Mb.
## ST16CH_3U31
## Number of contigs is 277. Cumulated length is 2.59Mb.
## ST16CH_3U42
## Number of contigs is 107588. Cumulated length is 42.55Mb.
## ST16CH_3U55
## Number of contigs is 64935. Cumulated length is 38.4Mb.
## ST16CH_3V10
## Number of contigs is 127380. Cumulated length is 43.98Mb.
## ST16CH_3V27
## Number of contigs is 97088. Cumulated length is 42.3Mb.
## ST16CH_3V30
## Number of contigs is 111162. Cumulated length is 43.07Mb.
## ST16CH_3V43
## Number of contigs is 98778. Cumulated length is 41.88Mb.
## ST16CH_3W21
## Number of contigs is 88367. Cumulated length is 42.08Mb.
## ST16CH_3W3
## Number of contigs is 100579. Cumulated length is 42.87Mb.
## ST16CH_3W9
## Number of contigs is 101796. Cumulated length is 42.46Mb.
## ST16DK_Biog_DK1
## Number of contigs is 128737. Cumulated length is 43.51Mb.
## ST16DK_Biog_DK15
## Number of contigs is 122579. Cumulated length is 43.55Mb.
## ST16DK_Biog_DK32
## Number of contigs is 109758. Cumulated length is 43.95Mb.
## ST16FR_Biog_FR1
## Number of contigs is 16. Cumulated length is 0.0Mb.
## ST16FR_Biog_FR31
## Number of contigs is 107398. Cumulated length is 42.18Mb.
## ST16FR_Biog_FR5
## Number of contigs is 85311. Cumulated length is 39.73Mb.
## ST16IRE_Biog_IR1
## Number of contigs is 81339. Cumulated length is 40.82Mb.
## ST16IRE_Biog_IR16
## Number of contigs is 110116. Cumulated length is 42.22Mb.
## ST16IRE_Biog_IR32
## Number of contigs is 109080. Cumulated length is 43.49Mb.
## ST16KA_Biog_K1
## Number of contigs is 3626. Cumulated length is 33.31Mb.
## ST16KA_Biog_K32
## Number of contigs is 107357. Cumulated length is 43.41Mb.
## ST16LE_Biog_L1
## Number of contigs is 112089. Cumulated length is 44.44Mb.
## ST16LE_Biog_L15
## Number of contigs is 118832. Cumulated length is 44.15Mb.
## ST16LE_Biog_L37
## Number of contigs is 113207. Cumulated length is 43.13Mb.
## ST16RU_Biog_R1
## Number of contigs is 109398. Cumulated length is 43.21Mb.
## ST16RU_Biog_R19
## Number of contigs is 98460. Cumulated length is 42.77Mb.
## ST16RU_Biog_R9
## Number of contigs is 109007. Cumulated length is 42.76Mb.
## ST16TN_Biog_TMW21F9
## Number of contigs is 5675. Cumulated length is 33.84Mb.
## ST16TN_Biog_TMW21H5
## Number of contigs is 179988. Cumulated length is 47.06Mb.
## ST17ISR_Biog_ISR35
## Number of contigs is 116975. Cumulated length is 43.54Mb.
## ST89CA_14CC22A
## Number of contigs is 92360. Cumulated length is 41.35Mb.
## ST89CA_24CC32B
## Number of contigs is 92561. Cumulated length is 41.48Mb.
## ST89CA_32CD21A
## Number of contigs is 121365. Cumulated length is 42.91Mb.
## ST90ORE_a12_3B_10
## Number of contigs is 66807. Cumulated length is 38.32Mb.
## ST90ORE_a12_3B_11
## Number of contigs is 67940. Cumulated length is 38.82Mb.
## ST90ORE_a12_3B_12
## Number of contigs is 59580. Cumulated length is 37.75Mb.
## ST90ORE_a12_3B_13
## Number of contigs is 4828. Cumulated length is 1.37Mb.
## ST90ORE_a12_3B_14
## Number of contigs is 85945. Cumulated length is 40.92Mb.
## ST90ORE_a12_3B_15
## Number of contigs is 107757. Cumulated length is 41.83Mb.
## ST90ORE_a12_3B_17
## Number of contigs is 51250. Cumulated length is 36.66Mb.
## ST90ORE_a12_3B_18
## Number of contigs is 99327. Cumulated length is 41.95Mb.
## ST90ORE_a12_3B_19
## Number of contigs is 44049. Cumulated length is 36.42Mb.
## ST90ORE_a12_3B_2
## Number of contigs is 86280. Cumulated length is 40.48Mb.
## ST90ORE_a12_3B_20
## Number of contigs is 54754. Cumulated length is 37.36Mb.
## ST90ORE_a12_3B_21
## Number of contigs is 54816. Cumulated length is 37.27Mb.
## ST90ORE_a12_3B_3
## Number of contigs is 85871. Cumulated length is 40.64Mb.
## ST90ORE_a12_3B_4
## Number of contigs is 74158. Cumulated length is 39.15Mb.
## ST90ORE_a12_3B_5
## Number of contigs is 74734. Cumulated length is 39.23Mb.
## ST90ORE_a12_3B_6
## Number of contigs is 59810. Cumulated length is 37.47Mb.
## ST90ORE_a12_3B_7
## Number of contigs is 77682. Cumulated length is 39.64Mb.
## ST90ORE_a12_3B_8
## Number of contigs is 69669. Cumulated length is 38.7Mb.
## ST90ORE_a12_3B_9
## Number of contigs is 72173. Cumulated length is 38.94Mb.
## ST90ORE_a12_4A_1
## Number of contigs is 55578. Cumulated length is 38.02Mb.
## ST90ORE_a12_4A_10
## Number of contigs is 73890. Cumulated length is 39.08Mb.
## ST90ORE_a12_4A_11
## Number of contigs is 88535. Cumulated length is 40.92Mb.
## ST90ORE_a12_4A_2
## Number of contigs is 60858. Cumulated length is 37.57Mb.
## ST90ORE_a12_4A_4
## Number of contigs is 80962. Cumulated length is 40.03Mb.
## ST90ORE_a12_4A_5
## Number of contigs is 83465. Cumulated length is 39.76Mb.
## ST90ORE_a12_4A_6
## Number of contigs is 64193. Cumulated length is 38.15Mb.
## ST90ORE_a12_4A_7
## Number of contigs is 76105. Cumulated length is 39.35Mb.
## ST90ORE_a15_2A_11
## Number of contigs is 28190. Cumulated length is 34.63Mb.
## ST90ORE_a15_2A_13
## Number of contigs is 85279. Cumulated length is 40.97Mb.
## ST90ORE_a15_2A_14
## Number of contigs is 31616. Cumulated length is 34.51Mb.
## ST90ORE_a15_2A_15
## Number of contigs is 53346. Cumulated length is 37.22Mb.
## ST90ORE_a15_2A_16
## Number of contigs is 42744. Cumulated length is 36.14Mb.
## ST90ORE_a15_2A_20
## Number of contigs is 46488. Cumulated length is 36.99Mb.
## ST90ORE_a15_2A_6
## Number of contigs is 81634. Cumulated length is 40.67Mb.
## ST90ORE_a15_2A_7
## Number of contigs is 46417. Cumulated length is 36.72Mb.
## ST90ORE_a15_2A_8
## Number of contigs is 53153. Cumulated length is 37.51Mb.
## ST90ORE_a15_3B_1
## Number of contigs is 76547. Cumulated length is 39.23Mb.
## ST90ORE_a15_3B_10
## Number of contigs is 71187. Cumulated length is 39.03Mb.
## ST90ORE_a15_3B_13
## Number of contigs is 65195. Cumulated length is 38.3Mb.
## ST90ORE_a15_3B_15
## Number of contigs is 65738. Cumulated length is 37.92Mb.
## ST90ORE_a15_3B_18
## Number of contigs is 55010. Cumulated length is 37.13Mb.
## ST90ORE_a15_3B_19
## Number of contigs is 84482. Cumulated length is 40.76Mb.
## ST90ORE_a15_3B_3
## Number of contigs is 97620. Cumulated length is 41.76Mb.
## ST90ORE_a15_3B_4
## Number of contigs is 107339. Cumulated length is 42.0Mb.
## ST90ORE_a15_3B_5
## Number of contigs is 99290. Cumulated length is 41.89Mb.
## ST90ORE_a15_3B_6
## Number of contigs is 91716. Cumulated length is 40.76Mb.
## ST90ORE_a15_3B_9
## Number of contigs is 72826. Cumulated length is 39.28Mb.
## ST90ORE_a15_4A_10
## Number of contigs is 43807. Cumulated length is 36.55Mb.
## ST90ORE_a15_4A_11
## Number of contigs is 41303. Cumulated length is 36.46Mb.
## ST90ORE_a15_4A_13
## Number of contigs is 74293. Cumulated length is 39.52Mb.
## ST90ORE_a15_4A_15
## Number of contigs is 78907. Cumulated length is 39.53Mb.
## ST90ORE_a15_4A_17
## Number of contigs is 79757. Cumulated length is 40.2Mb.
## ST90ORE_a15_4A_19
## Number of contigs is 77534. Cumulated length is 39.68Mb.
## ST90ORE_a15_4A_2
## Number of contigs is 37997. Cumulated length is 35.69Mb.
## ST90ORE_a15_4A_3
## Number of contigs is 88866. Cumulated length is 39.29Mb.
## ST90ORE_a15_4A_4
## Number of contigs is 45311. Cumulated length is 35.83Mb.
## ST90ORE_a15_4A_7
## Number of contigs is 72316. Cumulated length is 39.29Mb.
## ST92ISR_Ar_11g
## Number of contigs is 27859. Cumulated length is 35.7Mb.
## ST92ISR_Ar_11i
## Number of contigs is 41368. Cumulated length is 36.59Mb.
## ST92ISR_Ar_12d
## Number of contigs is 34988. Cumulated length is 36.13Mb.
## ST92ISR_Ar_12e
## Number of contigs is 39703. Cumulated length is 36.99Mb.
## ST92ISR_Ar_12f
## Number of contigs is 59767. Cumulated length is 38.47Mb.
## ST92ISR_Ar_15a
## Number of contigs is 30825. Cumulated length is 35.63Mb.
## ST92ISR_Ar_15c
## Number of contigs is 40626. Cumulated length is 36.11Mb.
## ST92ISR_Ar_16a
## Number of contigs is 34673. Cumulated length is 36.46Mb.
## ST92ISR_Ar_16h
## Number of contigs is 34910. Cumulated length is 34.68Mb.
## ST92ISR_Ar_17b
## Number of contigs is 57364. Cumulated length is 37.79Mb.
## ST92ISR_Ar_17d
## Number of contigs is 70770. Cumulated length is 39.2Mb.
## ST92ISR_Ar_17e
## Number of contigs is 57331. Cumulated length is 38.05Mb.
## ST92ISR_Ar_17i
## Number of contigs is 32802. Cumulated length is 35.79Mb.
## ST92ISR_Ar_17r
## Number of contigs is 19079. Cumulated length is 34.22Mb.
## ST92ISR_Ar_18b
## Number of contigs is 61888. Cumulated length is 37.97Mb.
## ST92ISR_Ar_19e
## Number of contigs is 53561. Cumulated length is 38.23Mb.
## ST92ISR_Ar_1b
## Number of contigs is 23600. Cumulated length is 34.36Mb.
## ST92ISR_Ar_1c
## Number of contigs is 29922. Cumulated length is 34.81Mb.
## ST92ISR_Ar_1j
## Number of contigs is 23380. Cumulated length is 35.42Mb.
## ST92ISR_Ar_21a
## Number of contigs is 35469. Cumulated length is 35.74Mb.
## ST92ISR_Ar_22f
## Number of contigs is 82596. Cumulated length is 40.68Mb.
## ST92ISR_Ar_2b
## Number of contigs is 41660. Cumulated length is 36.7Mb.
## ST92ISR_Ar_2c
## Number of contigs is 22917. Cumulated length is 33.97Mb.
## ST92ISR_Ar_2f
## Number of contigs is 52193. Cumulated length is 38.01Mb.
## ST92ISR_Ar_4b
## Number of contigs is 54125. Cumulated length is 38.08Mb.
## ST92ISR_Ar_4e
## Number of contigs is 4421. Cumulated length is 31.8Mb.
## ST92ISR_Ar_4f
## Number of contigs is 21705. Cumulated length is 34.87Mb.
## ST92ISR_Ar_4g
## Number of contigs is 38124. Cumulated length is 35.57Mb.
## ST92ISR_Ar_5a
## Number of contigs is 101408. Cumulated length is 41.24Mb.
## ST92ISR_Ar_5g
## Number of contigs is 10598. Cumulated length is 33.96Mb.
## ST92TK_2an
## Number of contigs is 95503. Cumulated length is 40.47Mb.
## ST92UK_A4
## Number of contigs is 100499. Cumulated length is 42.69Mb.
## ST92UK_Pla2
## Number of contigs is 106962. Cumulated length is 42.98Mb.
## ST92UK_XB16_1
## Number of contigs is 84919. Cumulated length is 39.75Mb.
## ST92YE_1
## Number of contigs is 5200. Cumulated length is 33.48Mb.
## ST92YE_4
## Number of contigs is 117291. Cumulated length is 43.05Mb.
## ST93IND_11a2
## Number of contigs is 132686. Cumulated length is 44.07Mb.
## ST93IND_28a1
## Number of contigs is 105599. Cumulated length is 42.27Mb.
## ST93URU_EE3b_1
## Number of contigs is 113601. Cumulated length is 42.98Mb.
## ST93URU_EE4a_1
## Number of contigs is 117500. Cumulated length is 43.34Mb.
## ST93URU_LC16_2
## Number of contigs is 143227. Cumulated length is 44.41Mb.
## ST94CNR_C3b1
## Number of contigs is 106157. Cumulated length is 42.57Mb.
## ST94KE_MF1a
## Number of contigs is 95252. Cumulated length is 41.37Mb.
## ST94KE_MI1a
## Number of contigs is 90383. Cumulated length is 41.34Mb.
## ST95CH_3B2a
## Number of contigs is 108650. Cumulated length is 42.47Mb.
## ST95CH_5A1a
## Number of contigs is 96578. Cumulated length is 39.21Mb.
## ST95UR_EC2_2
## Number of contigs is 94840. Cumulated length is 41.33Mb.
## ST99CH_28
## Number of contigs is 104688. Cumulated length is 42.65Mb.
## ST99CH_3A1
## Number of contigs is 44497. Cumulated length is 37.57Mb.
## ST99CH_3A10
## Number of contigs is 39996. Cumulated length is 36.32Mb.
## ST99CH_3A2
## Number of contigs is 64651. Cumulated length is 39.7Mb.
## ST99CH_3A4
## Number of contigs is 57307. Cumulated length is 38.68Mb.
## ST99CH_3A5
## Number of contigs is 41089. Cumulated length is 36.71Mb.
## ST99CH_3A6
## Number of contigs is 63313. Cumulated length is 38.18Mb.
## ST99CH_3A8
## Number of contigs is 77754. Cumulated length is 40.85Mb.
## ST99CH_3A9
## Number of contigs is 74543. Cumulated length is 39.94Mb.
## ST99CH_3B2
## Number of contigs is 61970. Cumulated length is 38.77Mb.
## ST99CH_3B4
## Number of contigs is 73957. Cumulated length is 40.07Mb.
## ST99CH_3B8
## Number of contigs is 98805. Cumulated length is 42.05Mb.
## ST99CH_3C4
## Number of contigs is 104833. Cumulated length is 43.41Mb.
## ST99CH_3C7
## Number of contigs is 55269. Cumulated length is 38.1Mb.
## ST99CH_3D1
## Number of contigs is 128076. Cumulated length is 44.82Mb.
## ST99CH_3D3
## Number of contigs is 88647. Cumulated length is 42.04Mb.
## ST99CH_3D5
## Number of contigs is 85274. Cumulated length is 41.05Mb.
## ST99CH_3D7
## Number of contigs is 92625. Cumulated length is 40.62Mb.
## ST99CH_3D8
## Number of contigs is 65072. Cumulated length is 39.52Mb.
## ST99CH_3F1
## Number of contigs is 31717. Cumulated length is 35.68Mb.
## ST99CH_3F2
## Number of contigs is 64550. Cumulated length is 39.43Mb.
## ST99CH_3F3
## Number of contigs is 43848. Cumulated length is 36.32Mb.
## ST99CH_3F4
## Number of contigs is 96692. Cumulated length is 41.54Mb.
## ST99CH_3F5
## Number of contigs is 113233. Cumulated length is 43.96Mb.
## ST99CH_3G2
## Number of contigs is 41076. Cumulated length is 37.53Mb.
## ST99CH_3G3
## Number of contigs is 49918. Cumulated length is 37.49Mb.
## ST99CH_3G6
## Number of contigs is 58771. Cumulated length is 38.57Mb.
## ST99CH_3H1
## Number of contigs is 94185. Cumulated length is 41.2Mb.
## ST99CH_3H3
## Number of contigs is 44091. Cumulated length is 36.87Mb.
## ST99CH_3H4
## Number of contigs is 51096. Cumulated length is 38.55Mb.
## ST99CH_SW39
## Number of contigs is 95695. Cumulated length is 42.27Mb.
## ST99CH_SW5
## Number of contigs is 95287. Cumulated length is 42.3Mb.
## STnnJGI_SRR4235061
## Number of contigs is 40087. Cumulated length is 38.92Mb.
## STnnJGI_SRR4235062
## Number of contigs is 49906. Cumulated length is 42.13Mb.
## STnnJGI_SRR4235063
## Number of contigs is 78322. Cumulated length is 44.98Mb.
## STnnJGI_SRR4235064
## Number of contigs is 49207. Cumulated length is 41.97Mb.
## STnnJGI_SRR4235065
## Number of contigs is 46850. Cumulated length is 41.55Mb.
## STnnJGI_SRR4235066
## Number of contigs is 42673. Cumulated length is 41.23Mb.
## STnnJGI_SRR4235067
## Number of contigs is 49499. Cumulated length is 42.67Mb.
## STnnJGI_SRR4235068
## Number of contigs is 58774. Cumulated length is 43.83Mb.
## STnnJGI_SRR4235069
## Number of contigs is 48911. Cumulated length is 42.91Mb.
## STnnJGI_SRR4235070
## Number of contigs is 47623. Cumulated length is 42.52Mb.
## STnnJGI_SRR4235071
## Number of contigs is 46216. Cumulated length is 41.05Mb.
## STnnJGI_SRR4235072
## Number of contigs is 45665. Cumulated length is 42.36Mb.
## STnnJGI_SRR4235073
## Number of contigs is 44870. Cumulated length is 40.78Mb.
## STnnJGI_SRR4235074
## Number of contigs is 42193. Cumulated length is 41.33Mb.
## STnnJGI_SRR4235075
## Number of contigs is 41783. Cumulated length is 40.33Mb.
## STnnJGI_SRR4235076
## Number of contigs is 56748. Cumulated length is 43.85Mb.
## STnnJGI_SRR4235077
## Number of contigs is 42479. Cumulated length is 41.64Mb.
## STnnJGI_SRR4235078
## Number of contigs is 38719. Cumulated length is 41.17Mb.
## STnnJGI_SRR4235079
## Number of contigs is 45246. Cumulated length is 41.83Mb.
## STnnJGI_SRR4235080
## Number of contigs is 48883. Cumulated length is 39.96Mb.
## STnnJGI_SRR4235081
## Number of contigs is 42027. Cumulated length is 40.39Mb.
## STnnJGI_SRR4235082
## Number of contigs is 44870. Cumulated length is 40.48Mb.
## STnnJGI_SRR4235083
## Number of contigs is 62563. Cumulated length is 43.77Mb.
## STnnJGI_SRR4235084
## Number of contigs is 59463. Cumulated length is 43.81Mb.
## STnnJGI_SRR4235085
## Number of contigs is 52361. Cumulated length is 43.21Mb.
## STnnJGI_SRR4235086
## Number of contigs is 41606. Cumulated length is 41.02Mb.
## STnnJGI_SRR4235087
## Number of contigs is 48650. Cumulated length is 42.16Mb.
## STnnJGI_SRR4235088
## Number of contigs is 44554. Cumulated length is 41.73Mb.
## STnnJGI_SRR4235089
## Number of contigs is 60325. Cumulated length is 43.26Mb.
## STnnJGI_SRR4235090
## Number of contigs is 57562. Cumulated length is 43.32Mb.
## STnnJGI_SRR4235091
## Number of contigs is 50312. Cumulated length is 42.17Mb.
## STnnJGI_SRR4235092
## Number of contigs is 44326. Cumulated length is 40.75Mb.
## STnnJGI_SRR4235093
## Number of contigs is 50101. Cumulated length is 42.26Mb.
## STnnJGI_SRR4235094
## Number of contigs is 64906. Cumulated length is 43.66Mb.
## STnnJGI_SRR4235095
## Number of contigs is 49460. Cumulated length is 41.87Mb.
## STnnJGI_SRR4235096
## Number of contigs is 50778. Cumulated length is 41.4Mb.
## STnnJGI_SRR4235097
## Number of contigs is 62767. Cumulated length is 44.04Mb.
## STnnJGI_SRR4235098
## Number of contigs is 45768. Cumulated length is 41.21Mb.
## STnnJGI_SRR4235099
## Number of contigs is 60652. Cumulated length is 43.74Mb.
## STnnJGI_SRR4235100
## Number of contigs is 51748. Cumulated length is 42.06Mb.
## STnnJGI_SRR4235101
## Number of contigs is 51709. Cumulated length is 42.08Mb.
## STnnJGI_SRR4235102
## Number of contigs is 132491. Cumulated length is 50.79Mb.
## STnnJGI_SRR4235103
## Number of contigs is 53196. Cumulated length is 42.42Mb.
## STnnJGI_SRR4235104
## Number of contigs is 66702. Cumulated length is 43.86Mb.
## STnnJGI_SRR4235106
## Number of contigs is 131398. Cumulated length is 50.44Mb.
## STnnJGI_SRR4235107
## Number of contigs is 36319. Cumulated length is 38.57Mb.
## STnnJGI_SRR4235108
## Number of contigs is 37125. Cumulated length is 39.7Mb.
## STnnJGI_SRR4235110
## Number of contigs is 128721. Cumulated length is 50.2Mb.
## STnnJGI_SRR4235111
## Number of contigs is 35350. Cumulated length is 41.31Mb.
## STnnJGI_SRR4235113
## Number of contigs is 44873. Cumulated length is 42.22Mb.
## STnnJGI_SRR5194475
## Number of contigs is 30784. Cumulated length is 39.81Mb.
## STnnJGI_SRR5194476
## Number of contigs is 41775. Cumulated length is 41.83Mb.
## STnnJGI_SRR5194477
## Number of contigs is 31906. Cumulated length is 41.04Mb.
## STnnJGI_SRR5194479
## Number of contigs is 26019. Cumulated length is 38.76Mb.
## STnnJGI_SRR5194481
## Number of contigs is 37295. Cumulated length is 41.16Mb.
## STnnJGI_SRR5194482
## Number of contigs is 46606. Cumulated length is 42.16Mb.
## STnnJGI_SRR5194483
## Number of contigs is 39345. Cumulated length is 40.78Mb.
## STnnJGI_SRR5194515
## Number of contigs is 36286. Cumulated length is 41.33Mb.
## STnnJGI_SRR5194532
## Number of contigs is 35341. Cumulated length is 38.6Mb.
## STnnJGI_SRR5194533
## Number of contigs is 50093. Cumulated length is 41.29Mb.
## STnnJGI_SRR5194534
## Number of contigs is 39602. Cumulated length is 41.27Mb.
## STnnJGI_SRR5194535
## Number of contigs is 42670. Cumulated length is 40.85Mb.
## STnnJGI_SRR5194587
## Number of contigs is 45917. Cumulated length is 40.67Mb.
## STnnJGI_SRR5194588
## Number of contigs is 32531. Cumulated length is 40.23Mb.
## STnnJGI_SRR5194589
## Number of contigs is 38143. Cumulated length is 40.59Mb.
## STnnJGI_SRR5194590
## Number of contigs is 34490. Cumulated length is 39.11Mb.
## STnnJGI_SRR5194591
## Number of contigs is 33729. Cumulated length is 39.93Mb.
## STnnJGI_SRR5194592
## Number of contigs is 38125. Cumulated length is 40.98Mb.
## STnnJGI_SRR5194593
## Number of contigs is 39822. Cumulated length is 41.37Mb.
## STnnJGI_SRR5194594
## Number of contigs is 33774. Cumulated length is 40.48Mb.
## STnnJGI_SRR5194595
## Number of contigs is 19547. Cumulated length is 37.09Mb.
## STnnJGI_SRR5194596
## Number of contigs is 44033. Cumulated length is 41.78Mb.
## STnnJGI_SRR5194605
## Number of contigs is 35238. Cumulated length is 40.76Mb.
## STnnJGI_SRR5194606
## Number of contigs is 49428. Cumulated length is 60.8Mb.
## STnnJGI_SRR5194607
## Number of contigs is 58484. Cumulated length is 41.8Mb.
## STnnJGI_SRR5829643
## Number of contigs is 18032. Cumulated length is 39.95Mb.
## STnnJGI_SRR5829673
## Number of contigs is 14546. Cumulated length is 39.96Mb.
## STnnJGI_SRR5829674
## Number of contigs is 16410. Cumulated length is 39.17Mb.
## STnnJGI_SRR5829692
## Number of contigs is 19414. Cumulated length is 40.37Mb.
## STnnJGI_SRR6447858
## Number of contigs is 39556. Cumulated length is 41.52Mb.
## STnnJGI_SRR6830963
## Number of contigs is 33327. Cumulated length is 40.73Mb.
## STnnJGI_SRR6830964
## Number of contigs is 37372. Cumulated length is 41.37Mb.
## STnnJGI_SRR6830965
## Number of contigs is 39312. Cumulated length is 41.49Mb.
## STnnJGI_SRR6830966
## Number of contigs is 35183. Cumulated length is 40.49Mb.
## STnnJGI_SRR6830967
## Number of contigs is 33343. Cumulated length is 40.36Mb.
## STnnJGI_SRR6830968
## Number of contigs is 27140. Cumulated length is 39.09Mb.
## STnnJGI_SRR6830969
## Number of contigs is 25533. Cumulated length is 38.99Mb.
## STnnJGI_SRR6830970
## Number of contigs is 32584. Cumulated length is 38.88Mb.
## STnnJGI_SRR6830971
## Number of contigs is 39584. Cumulated length is 39.27Mb.
## STnnJGI_SRR6831004
## Number of contigs is 48581. Cumulated length is 42.68Mb.
## STnnJGI_SRR6831008
## Number of contigs is 32884. Cumulated length is 40.72Mb.
## STnnJGI_SRR6831009
## Number of contigs is 32471. Cumulated length is 40.45Mb.
## STnnJGI_SRR6831010
## Number of contigs is 27291. Cumulated length is 37.72Mb.
## STnnJGI_SRR6831056
## Number of contigs is 33794. Cumulated length is 40.25Mb.
## STnnJGI_SRR7073263
## Number of contigs is 35289. Cumulated length is 41.25Mb.
## STnnJGI_SRR7073288
## Number of contigs is 37427. Cumulated length is 40.75Mb.
## STnnJGI_SRR7073289
## Number of contigs is 33326. Cumulated length is 40.44Mb.
## STnnJGI_SRR7073427
## Number of contigs is 32630. Cumulated length is 40.17Mb.
## STnnJGI_SRR7073430
## Number of contigs is 31064. Cumulated length is 39.33Mb.
## STnnJGI_SRR7073431
## Number of contigs is 43274. Cumulated length is 41.61Mb.
## STnnJGI_SRR7073594
## Number of contigs is 36785. Cumulated length is 41.24Mb.
## STnnJGI_SRR7073614
## Number of contigs is 33426. Cumulated length is 39.94Mb.
## STnnJGI_SRR7074464
## Number of contigs is 23730. Cumulated length is 37.54Mb.
## STnnJGI_SRR7074626
## Number of contigs is 35327. Cumulated length is 41.66Mb.
## STnnJGI_SRR7074627
## Number of contigs is 39966. Cumulated length is 41.98Mb.
## Switzerland_1999_ST99CH_3B6
## Number of contigs is 79955. Cumulated length is 53.36Mb.
## Switzerland_1999_ST99CH_3C9
## Number of contigs is 40832. Cumulated length is 40.46Mb.
## Syria_1992_SYK2
## Number of contigs is 84290. Cumulated length is 51.58Mb.
## Syria_1992_SYK3
## Number of contigs is 44275. Cumulated length is 41.49Mb.
## Syria_1992_SYK4
## Number of contigs is 84299. Cumulated length is 52.11Mb.
## Syria_1992_SYT2
## Number of contigs is 41861. Cumulated length is 41.16Mb.
## Syria_1992_SYT3
## Number of contigs is 39413. Cumulated length is 40.97Mb.
## Texas_1994_ST94TX_PA2a_1
## Number of contigs is 38037. Cumulated length is 40.62Mb.
## Texas_1994_ST94TX_PB2a_1
## Number of contigs is 60632. Cumulated length is 45.84Mb.
## Texas_1994_ST94TX_PB3a_1
## Number of contigs is 43122. Cumulated length is 41.79Mb.
## Texas_1994_ST94TX_PB4a_1
## Number of contigs is 63891. Cumulated length is 48.26Mb.
## Texas_1994_ST94TX_PC2a_1
## Number of contigs is 29574. Cumulated length is 40.09Mb.
## Texas_1994_ST94TX_PC3a_1
## Number of contigs is 67344. Cumulated length is 49.3Mb.
## Texas_1994_ST94TX_PD1a_1
## Number of contigs is 41279. Cumulated length is 42.06Mb.
## Texas_1994_ST94TX_PD4a_1
## Number of contigs is 35627. Cumulated length is 40.19Mb.
## Texas_1994_ST94TX_PF4a_1
## Number of contigs is 59568. Cumulated length is 45.27Mb.
## Texas_1995_ST94TX_PG3a_1
## Number of contigs is 36144. Cumulated length is 40.57Mb.
## Tunisia_2008_ST08TN_33_1_2
## Number of contigs is 2007. Cumulated length is 13.25Mb.
## Tunisia_2008_ST08TN_33_4_3
## Number of contigs is 84200. Cumulated length is 45.05Mb.
## Tunisia_2008_ST08TN_33_4_9
## Number of contigs is 110783. Cumulated length is 48.37Mb.
## Tunisia_2008_ST08TN_33_5_8
## Number of contigs is 82844. Cumulated length is 46.31Mb.
## Tunisia_2008_ST08TN_33_6_2
## Number of contigs is 85372. Cumulated length is 44.94Mb.
## Tunisia_2008_ST08TN_33_6_6
## Number of contigs is 104819. Cumulated length is 46.79Mb.
## Tunisia_2008_ST08TN_33_6_9
## Number of contigs is 114666. Cumulated length is 52.44Mb.
## Tunisia_2008_ST08TN_33_7_4
## Number of contigs is 95466. Cumulated length is 49.9Mb.
## Tunisia_2008_ST08TN_33_8_4
## Number of contigs is 93021. Cumulated length is 46.67Mb.
## Tunisia_2008_ST08TN_33_8_7
## Number of contigs is 89360. Cumulated length is 45.66Mb.
## Tunisia_2008_ST08TN_33_8_9
## Number of contigs is 122028. Cumulated length is 52.62Mb.
## Tunisia_2008_ST08TN_33_9_6
## Number of contigs is 92032. Cumulated length is 48.74Mb.
## Turkey_1992_TKA1a
## Number of contigs is 53032. Cumulated length is 43.32Mb.
## Turkey_1992_TKA1b
## Number of contigs is 46126. Cumulated length is 41.12Mb.
## Turkey_1992_TKA2a
## Number of contigs is 44124. Cumulated length is 40.51Mb.
## Turkey_1992_TKA2c
## Number of contigs is 95679. Cumulated length is 47.01Mb.
## Turkey_1992_TKV1
## Number of contigs is 79266. Cumulated length is 48.67Mb.
## Turkey_1992_TKV2a
## Number of contigs is 70615. Cumulated length is 44.48Mb.
## Turkey_1992_TKV2b
## Number of contigs is 67887. Cumulated length is 44.51Mb.
## Ukraine_1995_ST95UR_BIc_1
## Number of contigs is 40177. Cumulated length is 44.17Mb.
## Ukraine_1995_ST95UR_E2a_1
## Number of contigs is 25662. Cumulated length is 38.48Mb.
## Ukraine_1995_ST95UR_E2c_2
## Number of contigs is 30268. Cumulated length is 39.31Mb.
## Ukraine_1995_ST95UR_F1a_1
## Number of contigs is 35526. Cumulated length is 39.98Mb.
## Ukraine_1995_ST95UR_F1a_3
## Number of contigs is 34876. Cumulated length is 40.83Mb.
## Ukraine_1995_ST95UR_F1c_2
## Number of contigs is 39393. Cumulated length is 41.61Mb.
## Ukraine_1995_ST95UR_F2a_1
## Number of contigs is 33855. Cumulated length is 40.46Mb.
## Uruguay_1993_STUR93_EC1b_1
## Number of contigs is 42165. Cumulated length is 41.68Mb.
## Uruguay_1993_STUR93_EC1c_1
## Number of contigs is 36885. Cumulated length is 41.6Mb.
## Uruguay_1993_STUR93_EC2b_1
## Number of contigs is 34434. Cumulated length is 41.47Mb.
## Uruguay_1993_STUR93_EC3d_1
## Number of contigs is 41303. Cumulated length is 40.64Mb.
## Uruguay_1993_STUR93_ED3b_1
## Number of contigs is 60945. Cumulated length is 48.72Mb.
## Uruguay_1993_STUR93_EE1d_1
## Number of contigs is 91690. Cumulated length is 56.41Mb.
## Uruguay_1993_STUR93_EE2a_1
## Number of contigs is 42461. Cumulated length is 42.34Mb.
## Uruguay_1993_STUR93_EE3a_1
## Number of contigs is 36089. Cumulated length is 40.88Mb.
## Uruguay_1993_STUR93_EG4a_3
## Number of contigs is 34416. Cumulated length is 42.02Mb.
## Uruguay_1993_STUR93_EG4c_1
## Number of contigs is 73987. Cumulated length is 51.54Mb.
## Uruguay_1993_STUR93_LA4a_1
## Number of contigs is 35189. Cumulated length is 40.9Mb.
## Uruguay_1993_STUR93_LC1b_1
## Number of contigs is 33500. Cumulated length is 40.46Mb.
## Uruguay_1993_STUR93_LF2b_1
## Number of contigs is 44978. Cumulated length is 42.78Mb.
## Uruguay_1993_STUR93_LH4a_1
## Number of contigs is 32134. Cumulated length is 40.54Mb.
## Yemen_1992_YEQ2
## Number of contigs is 49447. Cumulated length is 42.28Mb.
## Yemen_1992_YEQ4
## Number of contigs is 49548. Cumulated length is 42.05Mb.assemb_stats = bind_rows(read_tsv(paste0(assemb_dir, "Stats_raw_assemblies.tab")),
read_tsv(paste0(assemb_dir, "Stats_filtered_assemblies.tab"))) %>%
left_join(metadata_file, by = c("Sample" = "ID_file"))
assemb_stats %>%
filter(!grepl("est contig", Estimate)) %>%
ggplot(aes(x = Value, fill = Assembly_type, col = Assembly_type)) +
geom_density(alpha = 0.6) +
theme_bw() +
facet_wrap(vars(Estimate), scales = "free") +
scale_fill_manual(values = c("#FF9F1C", "#2EC4B6")) +
scale_color_manual(values = c("#FF9F1C", "#2EC4B6")) 
assemb_stats %>%
filter(Assembly_type == "Filtered") %>%
filter(!grepl("est contig", Estimate)) %>%
group_by(Collection) %>%
mutate(Nb_per_collec = n()/4) %>%
filter(Nb_per_collec > 10) %>%
filter(Assembly_type == "Filtered") %>%
ggplot(aes(x = Collection, y = Value, fill = Collection)) +
geom_violin() +
theme_bw() +
facet_grid(rows = vars(Estimate), scales = "free") +
theme(axis.text.x = element_text(angle = 30, vjust = 1, hjust = 1)) +
labs(x = element_blank())
assemb_stats %>%
filter(Assembly_type == "Filtered") %>%
filter(!grepl("est contig", Estimate)) %>%
ggplot(aes(x = Value, fill = Assembly_type, col = Assembly_type)) +
geom_density(alpha = 0.6) +
theme_bw() +
facet_wrap(vars(Estimate), scales = "free") +
scale_fill_manual(values = c("#FF9F1C", "#2EC4B6")) +
scale_color_manual(values = c("#FF9F1C", "#2EC4B6")) 
nb_contig_thr = 1600
temp = assemb_stats %>%
filter(Assembly_type == "Filtered") %>%
filter(Estimate == "Nb contigs")
p1 = ggplot(temp, aes(x = Value, fill = Assembly_type, col = Assembly_type)) +
geom_density(alpha = 0.6) +
geom_vline(xintercept = nb_contig_thr, col = "#2EC4B6") +
theme_bw() +
labs(x = "Number of contigs",
y = element_blank(),
subtitle = str_wrap(paste0(sum(temp$Value >= nb_contig_thr),
" bad quality / ",
sum(temp$Value < nb_contig_thr), " good quality"),
width = 60)) +
scale_fill_manual(values = c("#FF9F1C")) +
scale_color_manual(values = c("#FF9F1C"))
length_thr1 = 30000000
length_thr2 = 40000000
temp = assemb_stats %>%
filter(Assembly_type == "Filtered") %>%
filter(Estimate == "Cumulated length")
p2 = ggplot(temp, aes(x = Value, fill = Assembly_type, col = Assembly_type)) +
geom_density(alpha = 0.6) +
geom_vline(xintercept = length_thr1, col = "#2EC4B6") +
geom_vline(xintercept = length_thr2, col = "#2EC4B6") +
theme_bw() +
labs(x = "Length",
y = element_blank(),
subtitle = str_wrap(paste0(sum(temp$Value <= length_thr1 | temp$Value >= length_thr2),
" bad quality / ",
sum(temp$Value > length_thr1 &temp$Value <= length_thr2), " good quality"),
width = 60))+
scale_fill_manual(values = c("#FF9F1C")) +
scale_color_manual(values = c("#FF9F1C"))
good_assemb = assemb_stats %>%
filter(Assembly_type == "Filtered") %>%
select(Sample, Estimate, Value) %>%
pivot_wider(names_from = Estimate, values_from = Value) %>%
filter(`Cumulated length` > length_thr1 & `Cumulated length` < length_thr2) %>%
filter(`Nb contigs` <= nb_contig_thr)
kept_assemblies = length(unique(good_assemb$Sample))
p3 = good_assemb %>%
pivot_longer(-Sample, names_to = "Estimate", values_to = "Value") %>%
ggplot(aes(x = Value)) +
geom_density(alpha = 0.6, col = "#2EC4B6", fill = "#2EC4B6") +
theme_bw() +
facet_wrap(vars(Estimate), scales = "free") +
labs(x = element_blank(), y = element_blank(),
subtitle = str_wrap(paste0("Combining the two filters retains ", kept_assemblies,
" good quality assemblies."),
width = 100))
top_row = cowplot::plot_grid(p1 + theme(legend.position = "none"),
p2 + theme(legend.position = "none"),
ncol = 2, labels = c("A", "B"))
cowplot::plot_grid(top_row, p3, ncol =1, labels = c("", "C"))
good_assemb %>%
write_tsv(paste0(assemb_dir, "Good_assemblies_stats.tab"))Mitochondrial complete assemblies
project_dir=/data2/alice/WW_project/
DATA_DIR=${project_dir}0_Data/
mito_gen_dir=${DATA_DIR}4_Mitochondrial_genome/
mito_blast=${mito_gen_dir}0_Mito_blast/
pop_str_dir=${project_dir}2_Population_structure/
mito_PS_dir=${pop_str_dir}1_Mitochondrial_genome/
cd ~/Software/mummer-4.0.0rc1/
mkdir ${mito_gen_dir}
mkdir ${mito_blast}
# Get list of good assemblies -> blast mitochondrial reference -> concatenate all results
#cut -f 1 /data2/alice/WW_project/0_Data/2_Denovo_assemblies/Good_assemblies_stats.tab | sed '1d' > /home/alice/WW_PopGen/Keep_lists_samples/Good_assemblies.args
#sbatch -p normal.168h --array=1-1195%50 Detect_gene_blast_array.sh /home/alice/WW_PopGen/Directories_new.sh /data2/alice/WW_project/0_Data/Zymoseptoria_tritici.MG2.dna.toplevel.mt+_only.fa /home/alice/WW_PopGen/Keep_lists_samples/Good_assemblies.args Illumina ${mito_blast}
# cat ${mito_blast}*blast.tab > ${mito_blast}Mitochondria.blast_results.tsvmito_blast_results_complete = read_delim(paste0(mito_blast, "Mitochondria.blast_results.tsv"), delim = " ",
col_names = c("sample_id", "gene", "qseqid", "sseqid", "pident", "length",
"mismatch", "gapopen", "qstart", "qend",
"sstart", "send", "evalue", "bitscore"))
mito_blast_results_per_contig = mito_blast_results_complete %>%
group_by(sample_id, sseqid) %>%
summarize(Min_coord = min(min(sstart), min(send)),
Max_coord = max(max(sstart), max(send)),
Length = Max_coord - Min_coord) %>%
ungroup()
complete_mito = mito_blast_results_per_contig %>%
group_by(sample_id) %>%
summarize(Total_length = sum(Length)) %>% ungroup() %>%
full_join(mito_blast_results_per_contig, .)%>%
mutate(Percent = 100*Length/Total_length) %>%
filter(Percent > 90) %>%
filter(Length > 30000)
#Writing the table out to export to the cluster
complete_mito %>%
dplyr::select(sample_id, sseqid) %>%
write_tsv(., paste0(mito_blast, "Complete_mitochondria_from_blast.txt"), col_names = F)##TO CHECK WHETHER USING ONLY THE LENGTH THRESHOLD WOULD RECOVER HETEROPLASMY!!!
#This section here is to check whether there are samples with two assembled mitochondria
complete_mito2 = mito_blast_results_per_contig %>%
group_by(sample_id) %>%
summarize(Total_length = sum(Length)) %>% ungroup() %>%
full_join(mito_blast_results_per_contig, .)%>%
mutate(Percent = 100*Length/Total_length) %>%
filter(Length > 25000)
ggplot(complete_mito2, aes(x = Percent, y = Length)) +
geom_point()
In the end, I would like to recover the structural variants based on the reference genomes. However, because the mitochondria is linear, spurious rearrangements could be detected when the breakpoint is created by the assembler to linearize the mitochondria. To prevent this from happening, I want to harmonize the breakpoints. The steps for this are:
- Extract the mitochondrial genome from the de novo assemblies
- Duplicate the mitochondrial genome so it “loops” and has each pieces several times
- Align the duplicated sequence on the reference sequence and identify breakpoints
- Identify new start and stop based on the reference sequence and reextract the mitochondrial genome based on these
project_dir=/data2/alice/WW_project/
DATA_DIR=${project_dir}0_Data/
mito_gen_dir=${DATA_DIR}4_Mitochondrial_genome/
mito_blast=${mito_gen_dir}0_Mito_blast/
mito_fasta=${mito_gen_dir}1_Mitochondrial_fastas/
pop_str_dir=${project_dir}2_Population_structure/
mito_PS_dir=${pop_str_dir}1_Mitochondrial_genome/
cd ~/Software/mummer-4.0.0rc1/
#mkdir ${mito_fasta}
#mkdir ${mito_fasta}0_De_novo
#mkdir ${mito_fasta}1_Tripled
#mkdir ${mito_fasta}2_Aligned
#mkdir ${mito_fasta}3_Harmonized
out_file=${mito_fasta}2_Aligned/All_circular.mcoords
echo -e "Sample Ref_start Ref_stop Denovo_start Denovo_stop" > $out_file
while read sample contig ;
do echo $contig > temp ;
# Initial extraction
python ~/Common_scripts/Filter_fasta.py --list temp --action keep \
--out ${mito_fasta}/0_De_novo/${sample}.mitochondria.fasta \
${DATA_DIR}2_Denovo_assemblies/${sample}.fasta ;
sed -i "s/>/>${sample}_/" ${mito_fasta}/0_De_novo/${sample}.mitochondria.fasta ;
length=$(awk 'FNR==2 { print length }' ${mito_fasta}/0_De_novo/${sample}.mitochondria.fasta) ;
if [ $length -lt 60000 ] ;
then
# Multiple and alignment
python ~/Common_scripts/Multiply_mito.py \
--out ${mito_fasta}/1_Tripled/${sample}.mitochondria.triple.fasta \
${mito_fasta}/0_De_novo/${sample}.mitochondria.fasta;
./dnadiff \
-p ${mito_fasta}/2_Aligned/IPO323_vs_${sample} \
${DATA_DIR}Zymoseptoria_tritici.MG2.dna.toplevel.mt+_only.fa \
${mito_fasta}/1_Tripled/${sample}.mitochondria.triple.fasta
awk -v sample=${sample} '{print sample, $1, $2, $3, $4}' \
${mito_fasta}/2_Aligned/IPO323_vs_${sample}.mcoords \
>> ${out_file}
fi
done < ${mito_blast}Complete_mitochondria_from_blast.txt
## scaf225
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf236
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf233
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf220
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf233
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf240
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf228
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf237
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf223
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf222
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf230
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf231
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf223
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf202
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf223
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf196
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf229
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf218
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf235
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf189
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf223
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf231
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf215
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf224
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf257
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf233
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf226
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf233
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf231
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf222
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf229
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf222
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf235
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf221
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf237
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf229
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf226
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf198
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf230
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf231
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf201
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf214
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf246
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf216
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf236
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf220
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf196
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf231
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf222
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf198
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf225
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf217
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf193
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf235
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf208
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf208
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf230
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf204
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf201
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf224
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf237
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf227
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf227
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf228
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf214
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf206
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf211
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf220
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf232
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf206
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf240
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf201
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf213
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf237
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf229
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf210
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf210
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf204
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf211
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf206
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf224
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf210
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf212
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf215
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf236
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf256
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf232
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf201
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf209
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf227
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf236
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf224
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf219
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf227
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf216
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf235
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf222
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf223
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf215
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf239
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf217
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf219
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf240
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf235
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf217
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf268
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf261
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf238
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf231
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf243
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf222
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf215
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf237
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf222
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf217
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf209
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf226
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf220
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf233
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf229
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf241
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf244
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf248
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf230
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf225
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf212
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf216
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf226
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf211
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf199
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf201
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf221
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf229
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf223
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf232
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf223
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf219
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf235
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf248
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf214
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf247
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf244
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf237
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf236
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf238
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf247
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf242
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf229
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf247
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf221
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf245
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf241
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf243
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf236
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf216
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf237
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf240
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf255
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf238
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf236
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf249
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf235
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf248
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf239
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf226
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf245
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf282
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf263
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf241
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf252
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf256
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf235
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf243
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf226
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf240
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf227
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf257
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf256
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf263
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf228
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf232
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf220
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf242
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf222
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf217
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf250
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf226
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf244
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf230
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf239
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf270
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf229
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf239
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf230
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf241
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf219
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf267
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf242
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf256
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf218
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf238
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf238
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf235
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf216
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf225
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf262
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf257
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf216
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf231
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf230
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf227
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf213
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf204
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf228
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf236
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf214
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf207
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf211
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf223
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf267
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf238
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf216
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf236
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf226
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf214
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf243
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf238
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf246
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf215
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf233
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf266
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf263
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf222
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf237
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf243
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf215
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf221
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf197
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf182
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf217
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf233
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf207
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf218
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf188
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf218
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf202
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf215
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf212
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf199
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf217
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf196
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf197
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf192
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf201
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf196
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf237
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf211
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf177
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf190
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf190
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf219
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf218
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf192
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf212
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf229
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf218
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf249
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf218
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf231
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf231
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf224
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf238
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf218
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf222
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf212
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf246
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf258
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf236
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf249
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf236
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf254
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf252
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf245
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf221
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf228
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf246
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf216
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf252
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf227
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf228
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf226
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf235
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf239
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf222
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf229
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf211
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf231
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf230
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf218
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf234
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf225
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf212
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf216
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf205
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf217
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf229
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf213
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf230
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf210
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## scaf97mito_aln = read_delim(paste0(mito_fasta, "2_Aligned/All_circular.mcoords"), col_names = T, delim = " ") %>%
rowwise() %>%
mutate(Min_coord_denovo = min(Denovo_start, Denovo_stop),
Max_coord_denovo = max(Denovo_start, Denovo_stop)) %>%
dplyr::select(-Denovo_start, -Denovo_stop)
temp = mito_aln %>%
group_by(Sample, Ref_start) %>%
#mutate(Min_start = min(Min_coord_denovo)) %>%
mutate(rank = rank(Min_coord_denovo, ties.method = "random")) %>%
filter(Ref_start == 1) %>%
filter(rank < 3) %>%
ungroup() %>%
select(-Max_coord_denovo, -Ref_start, -Ref_stop) %>%
pivot_wider(names_from = "rank", values_from = Min_coord_denovo)%>%
select(Sample, Start = `1`, Stop = `2`) %>%
mutate(Fragment = "First")
temp2 = mito_aln %>%
group_by(Sample, Ref_start) %>%
#mutate(Min_start = min(Min_coord_denovo)) %>%
mutate(rank = rank(Min_coord_denovo, ties.method = "random")) %>%
filter(Ref_start == 1) %>%
filter(rank > 1 & rank < 4) %>%
ungroup() %>%
select(-Max_coord_denovo, -Ref_start, -Ref_stop) %>%
pivot_wider(names_from = "rank", values_from = Min_coord_denovo) %>%
select(Sample, Start = `2`, Stop = `3`)%>%
mutate(Fragment = "Second")
fragments = bind_rows(temp, temp2) %>%
left_join(., complete_mito, by =c ("Sample" = "sample_id")) %>%
mutate(Length2 = (Stop - Start), Diff = (Length + 1) - Length2) %>%
group_by(Sample) %>%
mutate(rank = rank(Diff, ties.method = "random"))
fragments %>%
filter(rank == 1) %>%
mutate(Start = Start - 1) %>%
select(Sample, sseqid, Start, Stop) %>%
unite(col = "contig", c(Sample, sseqid), remove = F) %>%
dplyr::select(-sseqid) %>%
relocate(Sample, contig) %>%
write_tsv(., paste0(mito_fasta, "3_Harmonized/", "Reextracting_mitochondria.bed"), col_names = F)project_dir=/data2/alice/WW_project/
DATA_DIR=${project_dir}0_Data/
mito_gen_dir=${DATA_DIR}4_Mitochondrial_genome/
mito_blast=${mito_gen_dir}0_Mito_blast/
mito_fasta=${mito_gen_dir}1_Mitochondrial_fastas/
var_cal_dir=${project_dir}1_Variant_calling/
mito_SV=${var_cal_dir}6_Mito_SV/
pop_str_dir=${project_dir}2_Population_structure/
mito_PS_dir=${pop_str_dir}1_Mitochondrial_genome/
cd ~/Software/mummer-4.0.0rc1/
while read sample contig start stop ;
do
echo -e "${contig}\t${start}\t${stop}" > temp.bed ;
/home/alice/Software/bedtools getfasta \
-fi ${mito_fasta}1_Tripled/${sample}.mitochondria.triple.fasta \
-fo ${mito_fasta}3_Harmonized/${sample}.mitochondria.harmonized.fasta \
-bed temp.bed
./dnadiff \
-p ${mito_SV}IPO323_vs_${sample} \
${DATA_DIR}Zymoseptoria_tritici.MG2.dna.toplevel.mt+_only.fa \
${mito_fasta}3_Harmonized/${sample}.mitochondria.harmonized.fasta
done < ${mito_fasta}3_Harmonized/Reextracting_mitochondria.bed## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report file
## Warning: the index file is older than the FASTA file.
## Building alignments
## Filtering alignments
## Extracting alignment coordinates
## Analyzing SNPs
## Extracting alignment breakpoints
## Generating report filesample_list = fragments %>% select(Sample) %>% distinct() %>% pull()
file_list = paste0(mito_SV, "IPO323_vs_", sample_list, ".mcoords")
#list.files(path = paste0(mito_SV, "IPO323_vs_"), pattern = "*mcoords", full.names = TRUE)
coords_list = list()
for (i in c(1:length(file_list))) {
coords_list[[i]] = read_tsv(file_list[[i]],
col_names = c("Ref_start", "Ref_end", "Query_start", "Query_end",
"Ref_aln_length", "Query_aln_length", "Percent_ID",
"Ref_length", "Query_length", "Ref_cov", "Query_cov",
"CHROM", "scaf"))
}
coords_from_aln = do.call(rbind, coords_list) %>%
mutate(TEMP = gsub("_scaf", ":scaf", scaf)) %>%
separate(TEMP, into = c("sample_id", "scaffold"), sep = ":")
coords_from_aln %>% group_by(sample_id) %>% count() %>%
qplot(data =., x = n, geom = "histogram")
coords_from_aln %>% write_tsv(file = paste0(mito_SV, "All_complete_mitochondria.mcoords"))file_list = paste0(mito_SV, "IPO323_vs_", sample_list, ".snps")
snps_list = list()
for (i in c(1:length(file_list))) {
snps_list[[i]] = read_tsv(file_list[[i]],
col_names = c("POS", "REF", "ALT", "Ref", "POS_query",
"V1", "V2", "V3", "V4", "V5", "CHROM", "scaf"))
}
snps_from_aln = do.call(rbind, snps_list) %>%
mutate(TEMP = gsub("_scaf", ":scaf", scaf)) %>%
separate(TEMP, into = c("sample_id", "scaffold"), sep = ":") %>%
dplyr::select(CHROM, POS, REF, ALT, sample_id)
snps_from_aln %>% write_tsv(file = paste0(mito_SV, "All_complete_mitochondria.snps"))